Sonic Chronicles: Dark Island
by Kingstriker
Summary: Sequel to Sonic Chronicles: Sodor Chaos. A year after the many Sodor invasions of Sonic's enemies, a long forgotten threat resurfaces and is determined to disrupt the past, present and futures of Sonic and Thomas' worlds. When it seems Sonic's help is not enough, Thomas resorts to recovering an old friend from the legendary Magic Railroad and prove little engines can do big things.
1. King Boom Boo PT 1

_**Welcome everyone to the sequel to my first Sonic/Thomas crossover, and while this may have came sooner, I had other stories to work on and I needed to make sure I had all of my ideas written down. Deciding on certain Sonic villains is much harder than I thought, though it will be less than last time. I will go ahead and say that Mephiles from Sonic 06 will be featured in this, however it's not the one from the game, instead another one from an alternate universe, basically the one shown briefly in the archie comes in the Zone Jail.**_

 _ **Listed below are the Arcs for this story:**_

 _ **Arc 1: Sodor Boom Boos**_

 _ **Arc 2: Pirates On Rails**_

 _ **Arc 3: Bio-Island**_

 ** _Arc 4: Titans Of Sodor_**

 ** _Arc 5: Crystalized Darkness_**

 ** _Characters like Lyric, Metal Sonic, King Arthur and the Metarex may re-appear. I want this crossover to be much better than the previous and as you may see, I went a bit bigger._**

 ** _Reminder that like the previous one, not all villains will be completely in character, and the story will LOOSELY connect with the Sonic games, Sonic X, Sonic Boom or the comics. Some stuff will be altered for the story's sake. Anyways, enjoy!_**

* * *

Sonic Chronicles: Dark Island

 **ARC 1: Sodor Boom Boos**

Chapter 1: King Boom Boo PT 1

It has been a year since many of Sonic the Hedgehog's enemies have invaded the Island of Sodor and peace has been restored to the island. It also had been a year since the engines have seen Sonic and friends at all. But they knew the heroes were out defeating evil and keeping their parts of the world safe. However, after so long, evil would rise again, but it would become more than just a simple invasion. It would effect both Sonic's and Thomas' pasts, presents and futures.

 **Pumpkin Hill...**

Shade the echidna was continuing her travels around the planet alone, several times she has visited Station Square and the Island of Sodor to see her friends. But she never stayed long. One night, she had journeyed towards a mountainous area where she felt shivers go down her spine. All of the mountains had massive pumpkin heads on them with glowing yellow eyes and grins. She looked around at all the many pumpkins and tombstones. She did not feel comfortable.

"Woah, this place is really creepy...hmm...maybe someone lives around here." Shade wondered.

She kept her helmet on hoping she'd intimidate anyone who tried to harm her, it worked many times before. Leaping down a few ledges she found herself having to teleport to different mountains since there were large gaps. She knew if Knuckles was here, he could've just glided around. Her search for anyone turned up hopeless as she stood next to some railroad tracks where a train with a pumpkin face was located.

"That is one creepy train. It's so quiet around here, I guess no one really is around, just the cold." Shade rubbed an arm.

"BLEH!"

Suddenly Shade gets the shock of a lifetime when she is jolted back from a small ghost with large spirally eyes and sharp black teeth and claws jumping into her face and growing before fading away. Shade clutched at her beating chest before pulling out her leech blades.

"GHOSTS? I DON'T HAVE TIME FOR GHOSTS!" Shade growled.

She looked around, the ghost was gone. Thinking she was in the clear, she proceeded to warp to a different mountain, only for 3 ghosts to jumpscare her, but this time she swung her leech blades. The ghosts gasp and fade away just in time.

"Damn...who do these ghosts think they are?" Shade wondered.

She figured they must inhabit this place...and now she needed to get out of here. She suddenly heard laughing from several of them.

"IT ISN'T FUNNY!" Shade spun around trying to find them.

It was at that moment she could sense a ghost trying to sneak up on her, so she shut her eyes and swung a punch and nailed the ghost directly between it's large eyes. Seeing that she made her mark, she chuckled as the ghost rubbed it's face in agony.

"Yeah, didn't see that coming did ya?" Shade teased.

The boo gave her an annoyed look before rolling his eyes. Shade continued to speak.

"Next time you or those boos scare me, I'm destroying all these mountains." Shade threatened.

The Boo looked angered by that and growled. Shade puts away her leech blades and throws up her fists.

"You got something you wanna say you big-eyed creep?" Shade asked.

The Boo curled it's own claws into fists about ready to fight. As the two circled each other, Shade had no idea more boos were started to arrive...and soon was a much bigger one. Shade made the first move by lunging, only for the boo to move to the side and smack her upside the head. Shade turned around and kicked the boo in the face knocking it down. Suddenly she is sucker-punched by another boo, then bit on the arm by a third.

"UGH! GET OFF ME!" Shade demanded.

She grabbed the end of the biting boo and smacked him into the puncher. The first boo recovered and lunged again along with 5 more. Shade shut her eyes, no longer able to look them in the eyes and started to swing wildly with her eyes shut. Realizing she was hitting nothing, she opened her eyes to see the boos laughing at her foolishness.

"STOP LAUGHING AND FIGHT!" Shade demanded.

The boos looked at each other, then started to fuse together and formed into a Boo version of Shade, also with the spirally eyes and sharp teeth, the form was even her height.

"WHAT? HOW DID YOU GUYS...oh nevermind, GO AWAY!"

Shade lunged at her Boo version but the clone grabbed her arm then head-butted her. Before Shade could focus, the clone punched her twice in the head before sweeping her off her feet and laughed.

"Ugh...I'm not through." Shade grumbled.

She warped away and the clone looked around but couldn't find her. Then she appeared behind the clone and tackled it down where the two wrestled around for a minute before they heard a voice.

"STOP!"

The voice caused both to stop, Shade looked towards the direction of the voice to see a very large ghost with blue lips, yellow eyes and sharp claws looking down on them, he didn't look happy.

"Whoa...now that's big." Shade said.

"BOOS ENOUGH! LET HER GO!" He demanded.

The clone whines before splitting into the multiple boos. The large boo, known as King Boom Boo lowered down to Shade who was busy dusting herself off.

"Who are you?" He asked.

"I'm Shade the echidna, I was doing some traveling until your goons here started scaring me." Shade glared at the boos who stuck their tongues out at her.

King Boom Boo glared at his minions who were now ashamed.

"Ugh, we've been over this countless times...we don't scare guests anymore, don;t you remember what happened to the last 3?" King Boom Boo asked.

He looked over at 3 of the tombstones that were lined together, Shade shuttered. Looks like she had more bravery than they ever did. She looked towards the red sky and sighed.

"Well I should be going, I didn't plan on staying longer than I needed to." Shade said.

"HOLD IT GIRL!"

Shade stopped and shook in fright at the King's change of tone. She turned around getting a few giggles from the boos.

"What now?" Shade asked.

"Earlier we felt a strange disturbance around Pumpkin Hill, a few of my minions went to check it out, but they never returned. This place may be big, but it's hard for one of us to not get lost. Think you can help us locate them?" King Boom Boo asked.

Shade scoffed, after scaring and fighting with her, what made him think she was going to help them? Then again, it didn't seem like she could easily escape them, sure she could teleport, but checking her warp belt, she realized it needed to recharge for being used so much recently.

"I guess I have no choice...but how could I possibly find them? All the boos look exactly the same, are any of you even girls?" Shade asked.

Surprisingly, several raised their hands...yet they looked exactly like the others. Dropping the subject, she looked towards several of the nearby mountains for anything out of place. Maybe if she could locate the source of the disturbance, she may find some kind of clue. Before she started, a small explosion shook the ground she was standing on. They all saw some smoke rising from one of the mountains where the large pumpkin at the top was frowning.

"I'll check there!" Shade said.

She saw one of the underground rockets nearby and activated it so she could fly towards the mountain. As she got there...she saw nothing but a large crater where the explosion happened. No boos were around, well until a few seconds later when she's jumpscared again from behind. Shade turned around figuring it was the same Boo who tried to fight with her the first time.

"UGH! GO AWAY! I'M BUSY!" Shade growled.

But the Boo only laughed and pointed at her.

"Such foolishness." Came a voice.

"What?"

Suddenly Shade and the Boo are blinded by a bright light. Shade tried to make out what was causing it, but she only got a glimpse of crystalized spikes before she and the Boo vanished from Pumpkin Hill.

 ** _Island of Sodor..._**

Back on the Island of Sodor, nighttime had rolled around most of the engines were finished with their jobs. At Tidmouth Sheds, most of the engines were already sleeping, everyone except for Henry and Percy who were pulling the Flying Kipper and mail respectively. Unknown to the engines, they had new visitors. As Henry traveled towards the Mainland carrying the Flying Kipper, he looked up at the sky worried.

"Aw...it's going to rain soon, I need to hurry. I mean I'm not scared of the rain anymore...but it would still be nice to remain dry." Henry said.

Suddenly as he went around a bend, he was suddenly jumped by a ghost that faded right through him. Henry screamed and shut his eyes after seeing the large spiral eyes and sharp teeth. He braked hard and all the vans rammed into each other tossing around some of the crates of fish inside. Thankfully this time he didn't derail.

"WHAT WAS THAT?" Henry whimpered.

He was too scared to move on and kept his eyes closed in case it happened again. His driver and fireman looked around confused, they hadn't seen anything. At least until the driver takes another look outside the cab and gets jumped by the ghost as well as it fades away. The driver accidently tackles the fireman down.

"Sorry about that." The driver helped him up.

"No problem, that must have been what Henry saw just now." The Fireman figured.

"GHOSTS! I HATE GHOSTS!" Henry screamed.

While he panicked, the ghost, known as a Boo, was high in the air laughing at them. He wanted to try and possess someone but he needed a better victim. So he left to find someone else. Percy was still delivering the mail but was almost done.

"The sooner I get this done, the sooner I can rest easy." Percy smiled.

He was so used to taking the mail that he wasn't even tired. He knew he was doing the island a great service and that made him happy. Whistling into the night, he attracted the attention of a Boo who followed Percy. The Boo grinned evilly as he got ready to cause some trouble, however his plans were halted when it started to rain. Thunder and lightning boomed and flashed all over the sky and the Boo got scared. They didn't get much of this weather in Pumpkin Hill, not even around Aquatic Mine or Death Chamber. Knowing he needed to get out of the rain, he fazed right through one of the vans and saw the bags of mail.

"Hehehehe..." The boos giggled.

He started to throw the mail all around the van causing such a mess. Then he proceeded to do the same inside the other 2 vans. Every time Percy would stop at a station, the workers at the station would be baffled by the mess and had to sort them all back. This caused Percy to be late to every station left. On the way back to the sheds, Percy was thinking about the mess.

"They were all in the bags, how could they all have scattered around? Hmm...I guess I'll have to make sure they're completely tied up, I got lucky tonight, I know Sir Topham Hatt wouldn't be happy. He'll probably still talk to me in the morning." Percy sighed.

Suddenly, he hears ghostly laughing.

"What? Who is there?" Percy called out.

Suddenly the Boo floated up in front of him with a wicked grin, this scared Percy.

"AAHH! A GHOST!" Percy screamed.

He braked hard as the Boo laughed then went around to cab to scare his driver and fireman. The Boo wanted to do more than just scare them, he then shoved the two men out of the cab where they landed in a bush safely, then the Boo took control. He started to pull random levers and jolt Percy forwards.

"HEY! YOU CAN'T DO THAT!" Percy said.

The Boo ignored his cries and made Percy go faster and faster down the line, he was now considered a runaway. The Boo laughed as he blew on Percy's whistle, Percy could only watch as he raced down the line and around a few bends. He was coming very close to Tidmouth Sheds and saw that the turntable wasn't lined with his track.

"Oh no! HELP! STOP ME!" Percy whailed.

The other engines were awoken by Percy and were shocked to see him coming towards the turntable.

"SLOW DOWN PERCY!" Thomas yelled.

"I CAN'T! I'M BEING CONTROLLED BY A GHOST!" Percy yelled.

"A what?" Edward asked.

Just as the Boo was about to exit the cab, he is suddenly kicked in the face and launched onto the ground. The savior then applied Percy's brakes just in time and Percy stopped with his front wheels dangling above the bottom of the turntable.

"Phew." All the engines said at once.

Then they all turned towards the Boo who hissed at the new figure before fading away. The figure turned out to be Shade who came over to Percy's front.

"Hey Percy, long time no see." Shade smiled.

"Shade! You saved me? Thank you!" Percy said.

"No problem...think you can back up?"

"I can try."

Percy puffed backwards as hard as he could until his front wheels were back on the track, then the turntable turned to line up with his track. The other engines cheered Shade on as the Boo grumbled from nearby. He was then joined by 2 more and they all talked to each other, planning to cause more mischief tomorrow, and also get into contact with King Boom Boo. The Boos were allowed to hang around different parts of the world, as long they talked with King Boom Boo to let them know where they were resided or if the king needed them for something. As Percy went into his shed, Shade sat on his front deck.

"So Shade, what was that ghost? Do you know him?" Percy asked.

"Oh I got some explaining to do." Shade rubbed her head.

She had to remember to contact Sonic and his friends tomorrow...looks like the Island was in danger again. Nearbye, the engines and Boos were being spied on by the figure Shade could barely see, the crystalized menace evilly chuckled.

"This should be interesting...I've heard the stories about this place...and how that irritating blue hedgehog managed to save them countless times...and it included that little blue tank engine. I'll be watching for now...but I will plan a few surprises for them...I'll consider it a test. See you soon Sonic the Hedgehog and you'll meet me soon enough Thomas the Tank Engine."

With that the figure sunk into the ground and out of sight. With the blue blur's help it was time for Thomas to prove again that little engines could do big things.

 _ **To be continued...**_

* * *

 _ **Next time, Shade will seek the help of Sonic and co. to help capture the Boos, while at the time King Boom Boo gets word of the Island of Sodor and heads there to takeover it. Will his plan succeed or will Sonic have the final scare? STAY TUNED!**_


	2. King Boom Boo PT 2

Chapter 2: King Boom Boo PT 2

While Shade explained to the engines what happened earlier, the 3 Boos ventured out to explore for a new place to settle down. They were planning to claim the island as their new home while also finding a good base. Eventually they arrived at the docks to see Cranky unloading a few crates from a ship and putting them in a truck Salty was pulling. One of the ghosts decided to play a little trick. Seeing that Cranky was distracted, one of them flew next to him and waited for the right moment to scare him.

"Alright just one more crate and-AAAAAHHHHHHHH!"

Cranky shut his eyes tight as the Boo jumps at his face, then he is possessed by the Boo. Cranky's eyes and mouth turned to look just like the Boos. Before anyone could act, the possessed Cranky swung the last crate far into the sea and it floated away. Whatever was inside was now ruined. The other Boos laughed as Salty and the workers gasped on horror.

"Shiver me timbers, those ghosts just loss the shipment, but where did they come from?" Salty wondered.

The Boo left Cranky who blinked several times.

"AUGH! STAY AWAY FROM ME!" Cranky growled.

He swung his hook towards the ghosts but they flew down towards the workers who ducked and thankfully the Boos only brushed passed them. One headed for Salty who retreated backwards but one Boo caught up and possessed him. Salty's face changed and he started to race forwards down the line with the truck still connected. But as he came towards a bend, he was going so fast, the untied crates flew out of the truck and the truck itself snapped from Salty and crashed on the ground. The other Boos continued laughing and chased the possessed Salty out of the docks.

The other Boos decided to separate and cause their own kind of trouble, so they went across the island scaring anyone still awake. They even went far as to break people's windows, mess with signal box controls and possess troublesome trucks making them bump into each other. With Salty, the poor diesel was still racing along the line coming close to Henry who was on his way back home after a successful run with the Flying Kipper, it was almost morning and he was ready sleep in.

"Phew, finally I get the Kipper finished on time, Sir Topham Hatt will be very pleased." Henry smiled.

Then he heard Salty's horn.

"Salty?" Henry looked back.

His driver and fireman look back to see a scary sight, there was Salty with spirally eyes and sharp teeth.

"AHOY MATEY! I'M GONNA CRASH YE!" Salty smirked.

"WHAT?" Henry gasped.

Then Salty caught up to Henry and bumped him. Henry sped up trying to get away as the other Boos had arrived and laughed at Henry's misfortune. Henry shut his eyes again.

"NO NOT THE GHOSTS!" Henry screamed.

Salty bumped him again harder, then again, and again. Henry's wheels almost came off the track, but Salty's did. After another bang, Salty lost control and derailed, Henry was sent into a siding by a station and crashed straight through the buffers derailing as well. The Boo left Salty and the all the Boos laugh. Salty felt exhausted and Henry felt embarrassed. The Boos high-three each other before they find they were being spied on. There puffing up to them was Percy, he looked more upset than scared.

"Bleh?" The Boos were confused.

Percy looked over at Henry and Salty before glaring at the Boos.

"You know, you guys were scary before...but now I realized, you're not scary, you're just jerks!" Percy scowled.

This left the Boos baffled. Saying nothing else, Percy chuffed back to get Rocky. The Boos were left in shock, especially one who extended an arm wanting to get Percy's attention, but Percy ignored him. The other Boos looked out at the sky to see it getting bright.

"AAH!" One gasped.

Seeing the sunlight coming, the Boos scrammed for somewhere dark. They needed to get in touch with the king. Later that morning, Henry explained what had happened to him and Salty, Shade face-palmed.

"Ugh, I knew those ghosts would be trouble. I'm calling Sonic to sort this out right now." Shade said.

"Don't you think it's strange that Tails' security tower didn't alarm G.U.N.?" Thomas asked.

"I guess it doesn't detect them as a threat. They're more of an annoyance than anything else." Shade said.

"Ooh, I'd hate to see them again." Henry shuttered.

"Relax, it's not like they possessed you." James teased.

"For now." Henry said.

"The ghosts will cause nothing but trouble, I've heard the reports." Edward informed them.

"Well they better not mess with me while I'm pulling the express, I must go!" Gordon left the sheds.

"Be careful Gordon!" Thomas called.

"Aren't I always." Gordon said.

"Don't worry Thomas, ghosts don't come out during the day." Shade said.

"Well that's a relief...hey Percy you've been quiet. You alright?" Thomas asked.

Percy looked angry and just backed more into the shed, the others were confused.

"Um Percy?"

"I just need some time alone Thomas." Percy grumbled.

"Okay." Thomas said.

 **Station Square...**

Sonic the Hedgehog and his best friend Tails were eating some chilidogs outside Tails' workshop and admiring the bright sunny sky. Some chili felt onto Sonic's chest but he just swiped it away with an arm.

"Hey Sonic, did I tell you I have like 3 new inventions to work on this week?" Tails asked.

"Wow really? Why all in one week?" Sonic asked.

"I got a pretty long list, it builds up each month...I just need to figure out where I'll get some of the supplies, speaking of supplies, you still have that chaos emerald?" Tails asked.

"Right here!" Sonic pulled out the blue emerald.

"Sweet I might need it to power up some of the machines."

Nearbye was Big the cat who was fishing by the lake. Next to him, Froggy was just watching.

"Huh, Big has been there for awhile, but hasn't caught anything." Tails said.

"Maybe we should go talk to him." Sonic figured.

They went over to see Big smiling and humming a tune.

"Hey Big, caught anything?" Sonic asked.

"Nothing yet, but I'll catch something soon, isn't that right Froggy?" Big looked down at his friend.

"Ribbit!" Froggy hopped.

"You know I don't remember there being many fish in this lake you'd think they be scared off by all of Tails' engineering." Sonic joked.

"Ha ha." Tails rolled his eyes.

"I had a scary dream last night." Big spoke.

"About what?" Sonic asked.

"I was at Pumpkin Hill trapped behind a door, and all these ghosts kept scaring me and beat me up. It was horrible, then some strange figure came and freed me, only to start destroying the whole area." Big explained.

Sonic and Tails were surprised...and confused.

"Strange figure? Did you see what he looked like?" Tails asked.

"Well he kinda looked like Shadow." Big said.

"Shadow? People say I look like Shadow."

"Only because you're a faker!" They heard the familiar voice.

They turn to see Shadow standing a few feet away with his arms cross.

"Shadow, what are you doing here?" Tails asked.

"I got bored so I wanted to challenge the faker to a race." Shadow glared at Sonic.

"Hah, you're on!"

BEEP! BEEP! BEEP!

Tails' wrist communicator started to beep and he answered.

"This is Tails come in."

 **"Tails! The Island of Sodor is in trouble again, these strange ghosts have been disturbing the peace on this island, and I can't stop them on my own."**

"Ghosts...you mean the Boos? Oh no, those guys give me the creeps." Tails shuttered.

 **"Get Sonic, and if possible, bring Knuckles."**

"You got it, we'll be there soon!"

Once the called ended, Sonic spoke up.

"Tails what happened?"

"The Island of Sodor is being harassed by the Boos and Shade wants to stop them." Tails explained.

"Hmm, well we should head over to Pumpkin Hill first...and Knuckles can help us out with that. Tails, you get out to the island, I'll grab Knuckles and head over to Pumpkin Hill." Sonic ordered.

Tails nodded and flew off to get his Tornado-2. Sonic turns to Shadow.

"Shadow, want to help?"

"Hmph, last time you barely needed my help...why would I do it now?" Shadow scoffed.

"Sounds like Shadow is afraid of ghosts." Big teased.

Sonic had to contain his laughter when Shadow turned to the cat.

"You got something to say big guy?" Shadow stormed towards him.

Sonic slipped between them as Big got scared.

"Come on Shadow he was only joking."

"Hmph whatever, we'll have our race later."

Shadow warped away before Sonic and Big high-fived.

"Nice job Big, say you should come with us, you and Froggy."

"Really? I can help?"

"I don't see why not!"

"Yay!"

"Now go with Tails to the Tornado-2. No offense but you'd slow me down." Sonic nervously chuckled.

"No problem, come on Froggy." Big scooped him up.

So Sonic sped off to find Knuckles, no doubt he was guarding the Master Emerald.

 _ **Island of Sodor...**_

As the day went on, the engines were barely disturbed by the ghosts. Though several times Gordon was spooked by the Boos when he would enter tunnels, his constant slowing down caused him to nearly be late. At one point one Boo braved the sunlights and scared him as he went up his own hill, and made him stuck.

"Oh the indignity...now what?" Gordon sighed.

The Boo returned, trying it's best to stand the sunlight and possessed Gordon giving him the creepy face.

"HAH! You're too weak to get up this hill, let me take over." The Boos spoke.

The possessed Gordon actually managed to make it all the way up the hill just as Edward was coming from the other side with some trucks.

"Wow Gordon, you made it all by yourself...huh?"

Edward was immediately freaked out by Gordon's face and sped down the hill in fear. As they reached the top, the Boo released him and faded away.

"Huh? How did I..."

Gordon was at a lost for words as he raced down the hill, and made it to the station on time. Thomas was busy shunting some trucks around the mine where he once fell into years ago, he shuttered at the memories. He could faintly hear some kind of laughter coming from a small tunnel nearby. At first he thought one of the diesels was hiding around waiting to scare him. Just then, Mavis rolled up.

"Hello Mavis."

"Hello Thomas, I see you've been quick to shunt these trucks."

"Oh yes...say Mavis, do you hear something coming from that tunnel over there?" Thomas asked.

"Hmm, actually I do hear someting now, I'll go take a look." Mavis said.

Switching tracks, she headed towards the tunnel but could see nobody there.

"That's really odd, then who is-AAAAAAHHHHHHHHH!"

Mavis gets spooked, but instead of just her getting scared, the Boo was scared too. Turns out Mavis had found their temporary hiding spot and scared them by almost rushing in. Mavis laughs right after that. She backed towards Thomas who had came over.

"What happened?" Thomas asked.

"Apparently we scared each other." Mavis laughed.

The Boos grumbled as the two went away still laughing.

 _ **Angel Island...**_

Sonic found Knuckles who surprisingly was in a heated argument with King Boom Boo and the boos have somehow managed to find Knuckles and were accusing him of something. Sonic looked up at the sky to see it was getting very cloudy the less sunlight made it easier for the Boos to be out during the day. Sonic whistled and they all turned to him, Sonic tried not to look at the Boos' creepy faces.

"Okay enough already, what's going on?" Sonic asked.

"These ghosts are accusing me of wrecking Pumpkin Hill, apparently it was attacked after they send Shade out on some mission." Knuckles said.

"Oh yeah, some of the Boos are flying around the Island of Sodor and I needed your help and theirs." Sonic said.

"WHAT! WHY ME?" Knuckles said.

"Well because you know about these ghosts more than me and the others do, only you are crazy enough to go there for a reason." Sonic shrugged.

"You bet I am...WAIT WHAT! SHUT UP!" Knuckles growled.

"JUST ADMIT YOU ATTACKED PUMPKIN HILL!" King Boom Boo yelled.

"I DIDN'T ATTACK NOTHING!" Knuckles shot back.

"King Boom Boo I'm sure Knuckles couldn't have attacked Pumpkin Hill, how exactly was it attacked?" Sonic asked.

"After that female echidna left, we were bombarded with these large purple blasts that started to destroy the mountains and injure several of my minions. ONLY HE WOULD DO SUCH A THING!" The king point to Knuckles.

"SCREW OFF YOU STUPID GHOST! I'VE DEFEATED YOU BEFORE, I'LL DO IT AGAIN!" Knuckles shook a fist at him.

"Ugh, we don't have time for this. King Boom Boo can't you just call the Boos back?" Sonic asked.

"I would, but I don't know the location of this island you speak of." King Boom Boo said.

"Then we'll just have to get them back ourselves, plus Tails and Big should already be getting there." Sonic said.

"Wait you send Big? Seriously?" Knuckles groaned.

"Hey he wanted to help, poor guy barely gets to do anything these days." Sonic said.

Suddenly King Boom Boo felt a strange disturbance in his head and he growled.

"Eh?" The Boos looked confused.

"The missing Boos just sent me a signal...AH I KNOW JUST WHERE THEY ARE! THIS ISLAND OF SODOR MUST BE VERY INTERESTING IF THEY ALL WENT THERE! MAYBE IT CAN BE OUR NEW HOME!" King Boom Boo grinned evilly.

The Boos laughed evilly making Sonic and Knuckles angry, though the echidna was already pissed.

"NO!' Sonic shouted.

"Oh yes!" The King grinned.

With that all the ghosts warp away and Knuckles stomps a foot.

"DAMN! We need to get there fast!" Knuckles said.

"I got just the thing." Sonic pulled out the chaos emerald.

Knuckles looked back at the Master Emerald.

"Rouge I swear I'll punch you if you put one finger on that emerald." Knuckles whispered to himself.

Sonic teleported both him and Knuckles to the island.

 _ **Island of Sodor...**_

While the engines didn't have to deal with the Boos much during the day, the Boos themselves were getting tired of hiding around. Several times they attempted to float into the sunlight, only for it to burn them. However it was already starting to get late and that meant that Boos could finally come out of hiding. Shade and the remaining engines in the shed decided to stay there so they couldn't risk being spooked. Thomas, Percy, James and Henry were the only ones in the shed at the time.

"Here we go again, no doubt those Boos will be after us." Thomas said.

"Ugh...those things are so annoying." James groaned.

"I don't need to see them again." Henry backed up some more.

"Let's just hope for the best." Percy said.

"Hey what is that?" Shade asked.

She pointed to what looked like one Boo hiding behind a bush looking at them, Percy had had enough.

"I'll deal with him." Percy chuffed away.

"I'm coming too!" Shade got into his cab.

As the approached the Boo, the ghost looked a little embarrassed and sad...Percy was confused. It was the same Boo who first scared Shade and ruined the mail.

"Look, you ghosts need to go back to where you came from." Percy said.

The Boo still had it's sad look, Shade watched from the cab. Finally the Boo managed to speak.

"I'm sorry..." It said.

"What?" Percy said.

"I'm sorry for scaring you and your friends...we're just trying to find a newer home, not all the Boos, just some of us. We saw that your mountains are perfect for us to roam around, but the king wants to takeover the island." The Boo informed him.

Percy and Shade were surprised.

"So why aren't you helping him?" Shade asked.

"We don't have the desire to takeover...just exist somewhere besides the same places." The Boos sighed.

"How do we know this isn't a trick?" Percy asked.

"The other Boos are helping the other engines with their jobs." The Boo smiled.

Indeed they were, to make up for what they did, 2 Boos helped Edward get some troublsome trucks in line by scaring them straight. And when Gordon got stuck again, the Boos helped up him the hill, they were stronger than they looked. Heck they even listened to Toby tell them about past before coming to the railway.

"Well the king is wondering where they are!" Shade said.

"I know, so I called the king here so we could explain to him." The Boo said.

Shade face-palmed.

"That wasn't a good idea." Shade said.

Suddenly Sonic and Knuckles warp next to them.

"Ugh...I'm so not used to that." Knuckles said rubbing his head.

"SONIC! KNUCKLES!" Percy cheered.

"Hey Percy and Shade long time no see!" Sonic waved.

"S'up guys!" Knuckles nodded.

Then they spotted the Boo.

"THERE'S ONE!" Sonic pointed.

"WAIT HE'S ON OUR SIDE!" Shade stopped them.

"What?" Knuckles was shocked.

"Look we'll explain later."

Suddenly they see Tails and Big racing through the sky on the Tornado-2 and being chased by King Boom Boo, the Boos just looked confused.

"TAILS DOWN HERE!" Sonic yelled.

Tails dove towards them and Percy, Shade, Sonic and Knuckles raced back over to Tidmouth Sheds. The engines barely noticed Sonic's team as King Boom Boo hovered down laughing. All the Boos moved closer towards the engines. Henry was so frightened he couldn't even scream.

"KING BOOM BOO! THIS STOPS NOW, YOU WILL NOT TAKEOVER THIS ISLAND!" Sonic said.

"OH BUT I WILL! YOU CAN'T STOP ME!" King Boom Boo said.

Knuckle growled and jumped towards him with a punch but KBB turned invisible and Knuckles went right through him.

"DARN!" Knuckles gritted his teeth.

KBB teleported next to Sonic and whacked him away and damaged the Tornado-2. Tails had to fly out of the way of KBB's next hit and Shade managed to kick the ghost back. KBB then looked at the Boos.

"WHAT ARE YOU WAITING FOR? ATTACK!" He ordered.

But the Boos refused and just stared at him angrily. The talking Boo stayed close to Percy. KBB was baffled by their responses.

"WHAT?"

Percy then spoke up surprising all the engines.

"Listen King, they don't want to takeover this island, they just want a new area to explore and live...the island has some nice mountains for them to roam around in. And we won't let you change their minds."

The Boos cheered and the engines whistled. Sonic and his team got ready for KBB's next attack.

"UGH! USELESS ALL OF YOU! I'LL GET RID OF YOU ALL!" King Boom Boo yelled.

"HEADLAMPS ON!" Percy shouted.

All the engines sprung on their headlamps and Tails put on the headlamps of the Tornado. All the light blinded KBB.

"AAAAAAAUUUUUUUUGGGGGGGHHHHHHHH!" He whailed.

"NOW WHILE HE'S IN A SOLID FORM!" Shade said.

Sonic spindashed into the king and Knuckles clocked him in the face. Then Thomas and Percy rammed into him and pushed him down into the turntable well. Dazed, KBB struggled to get up, he had even shrunk down from all the sunlight. Sonic turned to Big.

"Hey Big, care for some fishing?" Sonic asked.

"I got this." Big said.

Thomas and Percy kept their headlamps on and the light shone over the turntable like a lazer grid. Big swung his finishing pole towards KBB and the hook snagged him on the back.

"RAWR!" KBB growled.

With a fierce tug, Big lifted KBB back in the light and he screamed.

"AAAAAAAUUUUUUUUUUUGGGGGGGHHHHHHHHHH! NNNNNNNNOOOOOOOOOOOOO! I'M GETTING OUT OF HERE!"

KBB vanished into a puff of smoke to parts unknown, everyone cheered. Edward, Gordon and Toby arrived at the sheds.

"You guys won't believe this, those Boos helped put my troublesome trucks in order." Edward said.

"And they helped me up the hill." Gordon said.

"And they even listened to my stories." Toby said.

The Boos felt great, and then turned to dog-pile on Big laughing. Froggy just watched not wanting to be a part of that. Finally Sir Topham Hatt arrived with Salty and Mavis.

"We saw everything from nearby and I must say Percy, Thomas, you're both really useful engines." Sir Topham Hatt smiled.

"Thank you sir." Thomas and Percy said at once.

The boos hovered Sir Topham Hatt laughing like children, this spooked the man.

"Ah yes well I suppose we'll be having some ghosts living here on the island as well." Sir Topham Hatt sighed.

"GHOSTS! LIVING HERE?" Henry shouted.

Without warning he backed all the way in the shed until his tender hit the wall. Sonic turned to his friends.

"Looks like another victory!" Sonic said.

"Yeah, only we barely did anything." Shade said.

"Well we may be here for awhile, I got to fix up the Tornado and upgrade the tower so it will detect King Boom Boo if he ever comes back." Tails said.

"I CAN'T STAY HERE! WHAT ABOUT THE MASTER EMERALD?" Knuckles shouted.

"As soon as I get the plane fixed I'll take you back." Tails offered.

"Thanks."

Sonic, Shade and Big turned to Thomas and Percy.

"Well Thomas, looks like I'm gonna be hanging here some more, it's been slow around my town, plus some weird entity is around blasting places up, maybe I could use your help again." Sonic said.

"I'll be ready!" Thomas whistled.

"Shade you in?" Sonic asked.

"Always."

"Big?"

"Yeah and so it Froggy!"

"Then that settles it!" Sonic shrugged.

Little did they know, the crystalized figure was watching them again...it's claws curled into fists before vanishing out of sight...

 ** _END OF ARC 1_**

 ** _To be continued in ARC 2: Pirates of Sodor..._**


	3. Captain Whisker & Johnny

_**This arc will only consist of one chapter instead of the usual 2 or 3 mainly because there wasn't so much I could do for these guys.**_

* * *

ARC 2: Pirates Of Sodor

Chapter 3: Captain Whisker & Johnny

A few days after King Boom Boo's attempt to take the island for himself, the Boos were happily flying around Sodor's mountains where they wouldn't bother the engines...unless it was Halloween. Though they would often come down to chat with the engines or join in any activities. It took some getting used to, but even the people around Sodor welcomed them. The Boo that had teased Shade often now hung around Percy. And one night, they decided to play a prank on Diesel who was talking to some of the others at the Dieselworks.

Shade, Sonic and the Boo rode in Percy's cab as they journeyed over to the Dieselworks. This was a payback prank after Diesel spooked Percy while he shunting trucks earlier. Percy did not like that one bit so he needed to get him back. Sonic of course was all in for the idea though Shade was hesitant.

"Ready ghost?" Sonic asked.

The Boo evilly laughed.

"I'll take that as a yes." Sonic nodded.

They hid behind a wall waiting for Diesel to stop talking to Arry and Bert, when the two left, Diesel was about to exit the building. Percy saw his chance and raced straight towards him, the Boo possessing him. When Diesel saw Percy, he immediately put on his brakes. What he saw was large spirally eyes and sharp black teeth on Percy's face.

"Percy? What happened to you?" Diesel asked.

"Nothing...JUST PLANNING YOUR DATE TO BE SCRAPPED!" Percy's possessed voice said.

Diesel had a look of horror on his face and Sonic and Shade were trying hard not to laugh.

"SCRAP? WHAT! SIR TOPHAM HATT WOULDN'T PLAN ME FOR SCRAP!" Diesel shrieked.

"I know...WHICH IS WHY I'M DOING IT MYSELF!"

Ghost Percy than ran straight for Diesel who started to race backwards into the Dieselworks confusing the other diesels.

"AHHH! PERCY IS GONNA KILL ME!" Diesel screamed.

As Percy came closer, he slammed on his brakes and then the Boos came out of person and jumpscared Diesel by growing huge and fading away. Diesel continued screaming as Arry, Bert, Paxton and Diesel 10 had begun to laugh at him. Diesel immediately stopped and was confused.

"Why are you laughing?" Diesel asked.

"Because it was only a prank!" Percy smirked.

Sonic and Shade fell out of the cab laughing their butts off. Diesel 10 used his claw to clap.

"Well done Percy...that was very clever." Diesel 10 laughed.

"Ugh...where did that ghost go anyway?" Diesel asked.

The Boo came over laughing too, much to Diesel's annoyance. The next morning, Percy told the other engines all about it.

"Well he got what he deserved." Thomas said.

"Looks like those Boos well come in handy after all." James said.

"Ugh...not for me." Henry shuttered.

"Oh come on Henry, they're not THAT scary." Gordon said.

"Well to you." Henry backed up a bit.

"So has Tails finished upgrading this tower yet?" Edward asked.

"Not yet...he has to go collect some more parts. I'm still trying to figure out who would destroy Pumpkin Hill. Knuckles couldn't have done that, it's not like him." Sonic said.

"You think the threat will arrive here?" Shade asked.

"Maybe...we just need to be careful." Sonic said.

"Well I did here some strange noises over night...but I couldn't tell where they were coming from." Shade informed.

"Interesting...heh, well whoever is doing this...they should know never to mess with me!" Sonic pointed to himself.

Shade smiled and shook her head. Meanwhile, over by the docks, Cranky was currently resting since he had nothing to do right now. He was facing the sea but had eyes closed so he was missing a mobian who was currently riding on her jet-ski watercraft. She seemed to be in a hurry to get to the island. When she got there, she jumped onto the dock panting, and of course getting weird glances from the workmen.

"WHAT ARE YOU ALL LOOKING AT MATES? Unless I got something on my shirt, nope I don't." She shrugged.

Salty comes by and sees her.

"Arr, who ye be lass?" Salty asked.

"Name's Marine the Raccoon mate!" Marine waved.

Meanwhile, Sonic was out on a run down the main line and was about to pass Gordon who was pulling the express. As he passed him, Sonic wagged his finger.

"Sorry Gordon, you're not fast enough!" Sonic smirked.

Sonic sped away and Gordon groaned.

"Hah...I'd be faster than him if he was a smelly old diesel." Gordon grumbled.

As Sonic eventually entered Henry's Forest, he heard a small crash and looked to his right, some trees had fallen over and were on fire.

"Uh-oh, this doesn't look good." Sonic said.

Heading towards the fire, he is smacked into by a tall green mech.

"AUGH! OUT OF THE WAY!" It yelled.

"Hey, what's the big idea?" Sonic rubbed his head getting up.

As soon as they laid eyes on each other they got in fighting positions.

"SONIC?"

"JOHNNY?"

Johnny who was once Captain Whisker's right-hand man was now a rogue and caused trouble on his own. But why and how did he get on this island, wasn't he from the Sol Dimension?

"Hey did you get here?" Sonic asked.

"Some random portal opened up and I decided to go through, I don't know who or what created it, but it was better than being trapped in a dimension with the cat princess. Oh and Whisker got through too, I'm trying to find that raccoon who started to mess with me." Johnny explained.

"Oh great...I know who you're-"

He's cut off when Blaze the cat comes flying over, fists lit with flames, and punches Johnny down a hill. Sonic could see the fire was spreading, so he quickly ran in a circle at super speed and created a whirlwind that spun around the area putting out all the fire. When he was finished he turned to see a shocked Blaze.

"BLAZE?"

"SONIC?"

Sonic immediately smiled.

"Long time no see Blaze, I assume you're trying to recapture these idiot pirates again?" Sonic asked.

"Of course, some strange portal opened up in my own throne room and pulled me in, thankfully I still have the Sol Emeralds with me. That's when I ran into Johnny, though I haven't seen Captain Whisker, but Johnny said both of them were planning to find Marine after she apparently 'pranked' them. But they got separated." Blaze explained.

"I thought Johnny ditched him."

"Oh they're not working together, they just have the same goal right now."

"I see, well let's finish off Johnny for good." Sonic said.

They both got ready when Johnny came racing angrily of the hill with such speed. Sonic and Blaze jumped out of the way, and then Sonic spin-dashed him onto his chest. Blaze then went to stomp onto his head but Johnny rolled out of the way and Blaze missed. Johnny got up and raced at Sonic who dodged out of the way of Johnny's fist. Johnny then took off trying to escape, only to be tackled by an unknown person.

"Wow...nice tackle Shade." Sonic held a thumbs up.

"It was nothing." Shade said.

Johnny growled and managed to knock her off before Blaze kicked him in the head making him tumble down the hill again, this time closer towards the tracks. Johnny got up sparking and cracking in a few places.

"HAH! YOU HAVEN'T WON YET! I'M NOT DONE!" Johnny yelled.

He had staggered back right onto the tracks not realizing who was racing down the line.

PEEP PEEP!

"CINDERS AND ASHES!" Thomas yelled.

Sonic, Blaze and Shade cringed hard when Thomas crashed straight into Johnny crunching him into pieces, ultimately killing him. Thomas had put on his brakes and stopped hard, Annie and Clarabel slamming into each other.

"OW! Thomas what was that?" Annie asked.

"Indeed, I heard a crunching noise." Clarabel said.

"I uh...oh no...I did it again." Thomas sighed.

Sonic and the girls came down smiling, though Shade was still wearing her helmet.

"No worries Thomas...you did the right thing." Sonic patted him on the side.

"Who was this?" Thomas asked.

"Oh just some rogue robot you don't need to worry about." Shade waved it off.

"Oh okay, hey Blaze!" Thomas smiled.

"Hello Thomas, how are you?"

"I'm doing fantastic, how's your dimension?"

"So far everything's been quite peaceful. Until these guys returned." Blaze sighed.

"We need to find Marine and Captain Whisker quick, no doubt they're around here." Shade said.

"Hmm...I think I know exactly where pirates would go on an island like this." Sonic rubbed his chin.

Suddenly some Boos race by taking no notice of them.

"Uh..." Blaze was lost.

"Long story, but now this island is haunted by bad-turned-good ghosts." Sonic shrugged.

"I see." Blaze was completely confused.

Over by the docks, Marine was busy talking with Salty about some of her past adventures. Cranky of course was glad he was busy working so he wouldn't have to just listen to their stories. It was bad enough having just Salty telling them. Eventually Sonic, Blaze and Shade arrive and wave to Marine.

"STREWTH IT'S SONIC, BLAZE AND SOME NEW GIRL! AHOY MATES!" Marine raced over.

"Marine! Good to see you!" Sonic said.

Marine hugged Sonic tightly before moving to Blaze and hugging her tightly, though she hesitated to hug Shade. Shade took off her helmet and smiled.

"I'm Shade, nice to meet you." Shade said.

Marine then decided to hug her tight anyway.

"Nice to meet you to mate!" Marine said.

"I assume you came through some kind of portal?" Sonic asked.

"Yeah how'd ya know? At the same time I was pranking those pirates and even tugged on Whisker's uh...whiskers." Marine giggled.

"Marine you know you shouldn't have done that." Blaze said sternly.

"Well I didn't think they would chase me, just get angry. But not only that...I heard they were planning on trying to get that Jeweled Scepter again, then go out and find some other treasure. I think I heard Whisker grumble something about digging all around this island while he was chasing me through the waters." Marine explained.

"So where could he be now?" Sonic wondered.

Suddenly he is knocked in the back of the head and crashes into Cranky. Everyone turns to see Captain Whisker there fuming as his fist came back to connect with his arm.

"Arr, I had to run into ye little punks again! I'm gonna get rid ye ONCE AND FOR ALL! THEN STEAL ALL THE TREASURE ON THIS ISLAND!" He yelled.

Salty backed away not wanting to be a part of this. But Sonic and the others knew they couldn't take him seriously.

"Oh come on captain...you lost before, you'll just lose again." Sonic said.

"I WILL WIN! I KNOW IT YOU BLUE SPIKY LANDLUBBER!" Whisker pointed at him.

"Yeah sure..." Shade teased.

"ARGH! HAVE AT THEE!"

Whisker opened part of his mouth and blew fire at them, but Blaze simply absorbed it. Whisker then fired his fists at them but Sonic spindashed one away while Shade took out her leach blades and damaged the other. Whiskers quickly drew back his fists before jumping and hitting the ground with such force making them all fall on the ground including the workmen. Cranky shook and Salty nearly derailed.

"Whoa, now that's an attack." Salty said.

"As long as I don't fall down again." Cranky muttered.

Whisker kept hitting the ground and the others couldn't focus. They needed to find a way to distract him.

"Ugh...we can't get near him." Sonic said.

"I can." Shade said.

Shade jumped high and over Whisker making him turn to her, Sonic and Blaze then lunged and tried to kick him down, but Whisker only staggered forward. One brave workmen tried to hit him behind with a crowbar but it had no affect. Cranky, Salty and Marine watched as Sonic and the girls fought with Whisker. Marine however, was also coming up with an idea.

"HEY CRANE, LEND ME YOUR HOOK MATE!" Marine yelled.

"Okay...and the name's Cranky!"

"Cranky? I guess you're cranky all the time eh?"

"No comment."

Marine grabbed Cranky's hook and hid it behind her.

"HEY WHISKER! OVER HERE!" Marine yelled.

Whisker turned to her and growled.

"YOU! I'M GONNA FINISH YE OFF YOU LITTLE RUNT!" He yelled.

As he charged at her, Marine threw the hook into Whisker's eye getting it stuck and Cranky lifted up and started to swing him around. Sonic and the girls watched in victory as Cranky then dropped him onto the rails so hard he became heavily damaged. Just then Percy was arriving with some trucks and unintentionally ran right over him, the trucks derailing in the process, but Percy stayed on the track. Luckily no one was hurt...except the dead robot pirate.

"What just happened?" Percy asked.

"You saved the day! We all did!" Sonic said.

"Nice work Cranky and Marine, that was a grand idea." Salty came back over.

"Oy, it was nothing. Thank the angry crane." Marine pointed up to Cranky.

"Eh...I did what I could." Cranky rolled his eyes.

"Now that that's over with, we should go celebrate." Sonic said.

"We just had a party after defeating King Boom Boo." Shade said.

"Hey I like parties, though I wonder if Tails will make it." Sonic said.

Marine then remembered something and grabbed Blaze in a hug.

"I JUST REMEMBERED IT'S BLAZE'S BIRTHDAY!" Marine yelled.

Blaze blushed seeing the surprise on Sonic and Shade's face.

"Whoa Blaze it's your birthday?" Sonic asked.

"It's not a big deal really. I just relax in my room all day while the guards do everything. Speaking of the guards, I really should be getting back to the Sol Dimension now that the mission is over with." Blaze said.

"Aw come on, your dimension hasn't been disturbed for a long time, not even by Eggman Nega, you deserve to relax somewhere that isn't there." Sonic grabbed her shoulder.

"What do you mean?"

"I mean, how about me, Shade and Marine give you a Sodor birthday party? You get to relax and finally see the sights around here. Finding out about those portals and other strange occurrences can wait." Sonic said.

"Oy, that sounds like a great plan!" Marine cheered.

"What do ya say Blaze, it wouldn't hurt right?" Shade said.

Blaze thought about it, she really had nothing else to do back at her castle...what harm could it be? Plus she had not even bothered to spend some time around the island. She saw Sonic putting on a shit-eating grin. This made Blaze blush and she let out a little chuckle.

"Very well." Blaze nodded.

"Sweet, and I know just the engine to give you a good time."

And so Sonic and the girls went to Knapford Station to wait for the engine.

"So is it Gordon?" Blaze asked.

"Nope, he thinks he's too busy to do stuff like this...shame." Sonic chuckles.

Just then Thomas arrived till with Annie and Clarabel.

"Hello again, I heard about everything that happened at the docks, that was very brave of you all to defeat that pirate." Thomas said.

"We couldn't have gotten the job done without you engines...as Sir Topham Hatt would say, you're really useful." Blaze smiled.

Now Thomas was blushing...and the blush became redder when Blaze comes over and gives him a small kiss on the check. Sonic, Marine and Shade just looked shocked, mostly Sonic. The hedgehog went to open one of Annie's doors and Blaze, Shade and Marine went in first. Once Sonic got in and shut the door, Thomas whistled and took off to give Blaze a tour, while Shade kept Marine distracted by listening to the raccoon's stories.

"By the way, what happened to the robots?" Thomas asked.

"Oh we threw them in the smelting pit." Sonic said.

"Oh...well that explains why Edward was so confused by the metal and green robot parts." Thomas said.

 _ **END OF ARC 2.**_

 _ **To be continued in ARC 3: Bio-Island...**_


	4. Biolizard PT 1

ARC 3: Bio-Island

Chapter 4: Biolizard PT 1

So for the rest of the day, everything went by pretty smoothly, Thomas showed Blaze and Marine all around the island. Marine constantly asked so many questions and Sonic agreed to try and answer them all. Shade talked with Blaze who was staring out the window. The feline was smiling and seemingly in thought.

"So Blaze, how are you feeling?" Shade asked.

"I actually feel rather calm for once, like a large weight has been lifted off my shoulders, for now." Blaze said.

"I guess being a princess isn't all that easy for you usually?" Shade asked.

"Well...it's been awhile since Eggman Nega has attacked, mabye he's given up or something. But I must always be ready, I'm still wondering about those strange purple portals...we really need to find who's causing them." Blaze said.

"Hmm, whoever is doing it, might have some connection to the island. Or at least know about what happened last year...it's pretty scary, and usually I'm not afraid of anything." Shade said.

"EXCEPT THE BOOS!" Sonic called out.

Shade flipped him off before Thomas blew his whistle.

"Alright everyone, there's a little surprise waiting for Blaze at Tidmouth Sheds. Though I'm not sure if all the engines will be there, they're still some jobs left to do on the island." Thomas said.

"That's alright Thomas, but really, you guys didn't have to do this." Blaze blushed.

"No, no you deserve it." Sonic laughed.

"Oy he's right you know!" Marine agreed.

"Shade might encounter some of the boos!" Sonic teased.

"SONIC!" Shade growled.

When they arrived at Tidmouth Sheds, they found only Percy, Edward, Henry and Tails who had just arrived back. Sitting in front of Percy was a table with food and a cake. Thomas stopped next to the sheds to let them out.

"Here we are Blaze, I know it's not much, but still you deserve to celebrate!" Sonic guided her towards the cake.

Deep inside Blaze was overjoyed, she didn't get to celebrate her birthday as big as most kids would. Marine ran over and grabbed Tails in a hug.

"TAILS MATE! SO GOOD TO SEE YOU!" Marine yelled.

"Nice to see you too, but you're choking me!" Tails gagged.

"Sorry mate."

The four engines whistled.

"Happy Birthday Blaze!" They all cheered.

Blaze blushed some more and giggled. Sonic wrapped an arm around her.

"Go on Blaze, have a slice of cake..." Sonic said.

Of course he already stole the first piece but Blaze didn't care. Much to Shade's annoyance, some Boos did join the party, Henry had to show some restraint. An hour later, Sonic was surprised when Shadow warped behind him.

"Alright faker, enough stalling...it's about time we have our race." Shadow said.

"Ugh...why now? We're in the middle of a birthday party." Sonic said.

"Who's?"

Blaze came over wiping some cake from her mouth with a napkin.

"Evening Shadow." Blaze waved.

"Same to you princess...and uh..." Shadow felt uncomfortable.

"I understand, what brings you here?" Blaze asked.

"Challenging faker here to a race." Shadow smirked.

"Go on Sonic, we'll be waiting for you here." Tails came over.

"Right on, alright Shadow...try to keep up. Let's race through the main line." Sonic said.

Sonic took off breaking the sound barrier and Shadow skated close behind him.

"Those two will never change." Tails sighed.

"Maybe it's for the best." Blaze shrugged..

The two hedgehogs raced down the line constantly passing each other. They came to a level crossing where Bertie was just crossing over forcing the hedgehogs to jump right over the whole thing.

"You've been practicing." Shadow said.

"Hey, this place is great for practice. You should come here more often." Sonic offered.

"Hmph."

After rounding a few bends and passing a few engines, Sonic remembered something.

"Hey Shadow, have you seen any strange portals appearing anywhere, or at least places being destroyed?" Sonic asked.

"No...why?"

"Well some strange portal sucked Blaze in bringing her and some villains here, that and someone attacked Pumpkin Hill, King Boom Boo accused Knuckles.

"I guess that is strange, but I'm sure it's none of my business." Shadow said.

"Ugh...you know sometimes I could use your help or advice." Sonic rolled his eyes.

"Hah...why would I ever give you advice faker?"

"Good point."

The two eventually see Wellsworth Station up ahead and Sonic smirks.

"Last one to make it to the platform is a rotten hedgehog." Sonic boosted ahead.

"Ugh." Shadow groaned.

But before they could reach it, a large explosion at the station propelled them back and they crash to the ground. Something had exploded behind the station and a purple inferno. Luckily no one was hurt.

"Whoa...what was that?" Sonic wondered.

"Some kind of strong power may have caused that." Shadow figured.

Investigating, the two find nothing there, just a small crater where the explosion was made.

"This is getting strange, first portals, now explosions." Sonic said.

"Huh...I guess we need to figure this out." Shadow looked towards the sky.

Sonic smirked and turned to him.

"You and me huh? That doesn't happen often." Sonic chuckled.

"I'm going alone...I can feel some strange energy, the same that's coming from this crater. I would rather work with Rouge and Omega than you." Shadow crossed his arms.

"Typical faker talk. I bet you're still mad after how Big teased you. Huh come to think of it, I haven't seen the guy since we defeated King Boom Boo." Sonic scratched his head.

"Well don't think I'm going to look for him, you're on your own, we'll finish this race later." Shadow said.

Before Sonic could retort Shadow had warped away. Sonic left to search for Big who could be anywhere right now. Back at the sheds, The engines and mobians were talking and wondering where Sonic and Shadow had gone off to. Blaze knew she'd have to return back to her dimension but at least wanted to say goodbye to Sonic before she left. Tails was talking with Shade and Marine.

"Well I can say this was a success, though I wish Sonic would hurry and get back here." Tails said.

"You never know with those two these says." Shade shook her head.

"Oy, maybe we should go find them." Marine suggested.

"Nah, we'll probably fail to find them." Tails said.

"Hey I just remembered something...where's Big?" Shade asked.

"I haven't seen him, maybe went fishing somewhere." Tails thought.

Finally Sonic did arrive looking confused.

"Hey guys, have you noticed Big has been gone?" Sonic asked.

"We were just talking about that." Shade said.

"Hmm...oh hey Blaze I guess you got to for now?" Sonic figured.

Blaze came over eating the last slice of cake while Marine followed her.

"Yeah...I need to make sure everything is still in place back at the castle. Sonic...thank you for all of this. It's been nice to see you again." Blaze said.

"Same here Blaze." Sonic nodded.

The two shook hands before Blaze summoned the Sol Emeralds. Marine gave Sonic a quick tight hug before she and Blaze are warped back to their dimension. Just as they left...Thomas started to feel a strange sense.

"What's wrong Thomas?" Percy asked.

"Everyone noticed Thomas looked rather...troubled. He was frowning and his eyes were darting left and right.

"Uh...it's not a big deal." Thomas said.

Before anyone could say anything, Thomas uncoupled from Annie and Clarabel and raced off down the line. The engines look at each other and the mobians do the same.

"That was strange." Tails said.

"Huh, I wonder what's upsetting him?" Edward said.

"Maybe I should go check on him." Percy said.

"I'll go with you." Shade said.

So Shade hopped into Percy's cab and they set off to look for Thomas. Though it may have seem like a random location, Big had ventured towards an old pair of buffers at the end of a line...and was being trapped. In front of him was the strange crystalized figure from before. The figure had backed Big towards the buffers.

"Why are you trying to harm me?" Big whimpered.

"Because you are in the way of my goal. NOW STEP ASIDE!" The figure growled.

"No...you have Froggy! Give me back Froggy!" Big said.

"Hah...you're friend will be my hostage."

The figure had Froggy trapped in a small icy orb, though Froggy didn't seem to be uncomfortable. Big could not believe Froggy was trapped, he figured trying to use his lure as a weapon would be useless against this person. Though Big thought this figure looked familiar.

"Hey...you look like Shadow, but all icy." Big said.

Before the figure could answer, they heard quick chugging and looked to see an angry Thomas coming straight for them. Big ran to the side of Thomas and the figure just stared at the engine in surprise.

"You stay away from those buffers, they're very special. Who are you?" Thomas said.

"That's none of your concern." The figure said.

"You're a hedgehog, and you look like Shadow...only...made out of crystals?" Thomas figured.

"Hmph, you seem to care about these buffers specifically, what's so special about them? I could sense some strange energy behind them." The figure walked over to them.

Thomas knew what would happen if he got closer, so he was unable to stop him.

"STOP! I'LL NEVER TELL YOU!" Thomas sneered.

"Oh really, well I guess I'll have to find out myself. And this frog will have to perish!" The hedgehog evilly laughed.

"FROGGY!" Big yelled.

Just then Percy and Shade arrive, Shade immediately sees the hedgehog as a threat and runs towards him.

"YOU THERE! STOP!" Shade growled putting on her helmet.

"Thomas what's going on?" Percy asked.

"YOUR DESTRUCTION SOON, THAT'S FOR SURE!" The figure growled.

Shade went to slice at him with her leech blades but the figure floated into the air.

"Hehe foolish beings...I've been watching all the chaos that has happened since last year...and I seek to destroy what keeps this island afloat and crush your lives into dust! I assume these buffers have something to do with it huh? Well then, Thomas is it? I'll be studying you more for now, your friends however...won't be so lucky as you!" The crystalized hedgehog glared at Percy.

"You leave my friends alone!" Thomas wheeshed steam.

"Hah! You may have thwarted past villains, but you won't stop me." He said.

The figure hadn't noticed Big making his way behind him with his lire, and swung it catching the small orb that Froggy was inside of and caught him.

"I HAVE YOU FROGGY!" Big cheered.

"WHAT?" The figure looked at him.

Suddenly he's kicked in the face by a certain black hedgehog and onto the ground.

"SHADOW!" Everyone gasped.

"Hmph, guess you really did need my help for once Thomas." Shadow smirked.

The figure got up and got everyone's attention.

"UGH...I DON'T HAVE TIME TO DEAL WITH ALL OF YOU! YOU SHOULD BE MORE WORRIED ABOUT YOUR FRIENDS AT THE SHEDS!"

"What?"

Suddenly they heard a loud roar as a massive purple portal opened up in the sky above Tidmouth sheds, a large red and black lizard that was seemingly on life support fell from the sky surprising the engines and landed right onto the turntable destroying it. It's large tails swung around and destroyed the roof of the sheds. Sonic and Tails had been knocked away by the landing and were currently unconscious.

"What is that?" Shade asked.

"It's big!" Percy gasped.

"It's black and red like Shadow."

Everyone turned to Shadow who was gripping his head...some memory was coming back.

"No...it can't be..." Shadow gasped.

Everyone then notices the figure was gone.

"What is it Shadow?" Thomas asked.

"It's the prototype of...me...the Biolizard."

 _ **To be continued...**_


	5. Biolizard PT 2

Chapter 5: Bio-lizard PT 2

Edward and Henry were trapped in the sheds by the damage and even Tails' Tornado-2 was damaged. The Biolizard turned around and roared at the engines. Sonic and Tails had just woken up and saw the beast.

"Huh? The Biolizard...but we killed that thing long ago...didn't we?" Sonic rubbed his head.

"Whoa, that thing looks pretty creepy up close." Tails gasped.

"Stand back Tails, I'll have to get rid of it this time...though this reminds me, where is Shadow?" Sonic wondered.

"Everyone is disappearing now." Tails said.

Sonic then noticed the Biolizard was glowing a strange purple...it never did that before. Even it's eyes were purple.

"Hey Tails, something's wrong with it, you see that purple glow?"

"Yeah."

"Well...whatever it is, I'll put a stop to it." Sonic got ready.

The Biolizard turned to Sonic and Tails and was about to fire it's electric orbs when Thomas, Percy, Shade, Shadow and Big arrived. Thomas and Percy gasped when they saw how big the Biolizard was, it was much bigger than them.

"EDWARD! HENRY! YOU GUYS ALRIGHT?" Thomas yelled.

"YES! BUT WE'RE TRAPPED!" Edward shouted.

"This is just a nightmare, just a nightmare right?" Henry hoped.

"Sorry Henry this is real." Edward sighed.

Shade and Big raced over to Sonic and Tails while Shadow just watched from nearby, he was too busy in shock. He only remembered little bits of the fight with the Biolizard...he felt some kind of connection to it. The biolizard roared again before blasting at the tank engines. Thomas and Percy backed onto different lines to avoid the blasts. Sonic needed to distract it.

"HEY LIZARD, OVER HERE!" Sonic yelled.

The Biolizard started to rotate around as Sonic raced in a circle, all the Biolizard could do was rotate and tried to slam it's tail on Sonic but he was too quick. Sonic raced around the lizard as it continued to rotate around hoping to squish Sonic. Shade and Tails noticed Shadow not even helping.

"Um Shadow, while Sonic is distracting it, you could be warping up to the core of the life-support system and damage him!" Shade said.

Shadow shook his head trying to get rid of his shock and finally decided to join in. However as he lunges towards the lizard, a strange purple blast hits him from behind and he gets launched much faster at the lizard, only to get smacked by the Bio-lizard's neck flinging him into the rubble of the sheds.

"SHADOW!" Tails yelled.

"He'll be fine, he's been through much worst." Sonic assured.

"RRRRRRRRRRRROOOOOOOOOOOOOOOOAAAAAAAAAAAAARRRRRRRRRRRRRRRR!" The bio-lizard screeched.

The bio-lizard then tires out and starts to exhale it's breath. Sonic found his cue to slide up the cords and home-attack into the core damaging him. The lizard screamed in pain before angrily rotating around and shots some orbs from it's mouth. Tails went to check on Shadow while Shade joined Sonic. Big stayed close to the engines clutching Froggy.

"Will we beat that thing?" Big asked.

"I'm sure of it, Sonic once told us how Shadow defeated it long ago, before it took their super forms to kill it...though it cost Shadow's life." Thomas explained.

"At least he's back now." Percy said.

The Biolizard's tail came down towards Thomas and Percy who backed away, the impact caused the rails to be damaged and form a ramp-like form. This gave Thomas an idea.

"SONIC, GIVE ME THE CHAOS EMERALD!" Thomas shouted.

As Sonic raced around the lizard, he tossed the blue emerald into Thomas' cab.

"Thomas, you sure you know what you're doing?" Percy asked.

"I have to take a risk." Thomas said.

Thomas charged towards the ramp-like rails and shot up into the air before-

"CHAOS CONTROL!"

Thomas warped into the air and charged straight into the core with the emerald's power. Pain from being hit by a steam train caused the Biolizard's extreme amounts of pain. Thomas had bounced off the core and warped back on the rails. Percy could not believe what he just saw.

"Thomas! That was incredible!" Percy shouted.

Shade then ran with Sonic as the Biolizard was still stunned from the hit, Sonic threw Shade into the air and she flipped straight towards the core and stabbed her leech blades into it.

 **"RAAAAAAAAAAAAAAAAAAAAAAWWWWWWWWWWWWWWWWWWWRRRRRRRRRRRRRRRRR!"** The Biolizard screeched some more.

Tails had cleared the rubble off of Shadow who was just waking up.

"Shadow you okay?" Tails offered his hand.

Shadow pushed the hand away and got up himself scoffing.

"Hmph, I'm fine. I guess Sonic and Shade are handling the Biolizard?" Shadow assumed.

"And Thomas." Tails added.

"What?"

Shadow watched as Thomas repeated his action by warping into the air and charging into the core. Shadow remembered that Thomas was able to do such incredible things.

"I see, well I'll put a stop to all of this." Shadow nodded.

Seeing the Biolizard tiring out some more, Shadow skated passed Sonic and Shade nearly knocking them over and avoiding the final slam of the bio-lizard's tail before the lizard released some orbs all around him and causing Shadow to be lifted up and spun around. While Sonic and Shade were stuck spazzing around in the air avoiding the orbs, Shadow managed to maneuver passed them and home-attacked the core.

SLAM!

 **"RRRRRRRRRRRRRRRRAAAAAAAAAAAAAAAAAAAAAAAAAAWWWWWWWWWWWWWWWWWWWWWWWWWRRRRRRRRRRRRRRRRRRRRRRRRR!**

THOOOOOOOOOOOOOOOOOOOOOOOOOOOOOM!

The Biolizard let out it's dying roar before slamming it's head on the ground. All the slamming had destroyed the ground around the sheds and even the vibrations had derailed Edward and Henry inside the sheds. Gordon, James and Emily arrived after hearing all the commotion from the sheds and even Sir Topham Hatt arrived.

"Whoa...what is that?" James asked.

"Long story." Sonic sighed.

"Oh no the sheds!" Gordon gasped.

"Now where will we sleep?" Emily wondered.

"Wait...where are Edward and Henry?" Sir Topham Hatt asked.

"HERE SIR!" They both yelled from inside the sheds.

"Oh dear...what a mess this is? But where did this come from?" Sir Topham Hatt asked.

"It just appeared from the sky through some purple portal." Sonic explained.

"But who do we know that could send stuff from the dead?" Tails asked.

"And Shadow what the hell was that? You just get launched into the lizard without any explanation?" Sonic turned to the ultimate lifeform.

"All I remember is being hit by something behind me." Shadow said.

Shade turns to Thomas who looks confused and nervous.

"Thomas...what was so special about those buffers from earlier?" Shade asked.

Thomas immediately looked resistant, so did the other engines. This confused the mobians, even STH was straightening his jacket out of awkwardness.

"Thomas...is there something you're not telling us...ALL OF US?" Sonic sneered.

Suddenly the Bio-lizard exploded into little purple particles that faded away...much to everyone's shock.

"It was fake, or like some kind of clone." Tails said.

"Ugh...this is all too confusing." Sonic said.

Thomas moved closer to the mobians, a serious look on his face.

"I'll explain what could be going on." Thomas sighed.

"Good." Sonic nodded.

A while later, STH held a meeting in front of the sheds with the mobians and engines...Shadow only stayed so he could get revenge on whoever had hit him. Workmen had managed to move the rubble away from the destroyed engines sheds and free Henry and Edward before Rocky put them back on the tracks.

"Okay everyone, I know a lot of confusion and delay has befallen this island today, and we're are going to address everything that happened so we can fix this. First thing, you engines will unfortunately have to find new places to sleep until the sheds are repaired. We don't know how long it will be before you can sleep here though." STH explained.

The engines groaned in annoyance.

"Great, now I can't get a good night's sleep for the express tomorrow." Gordon groaned.

"Uh Gordon I'm sure we have other things to worry about." Edward said.

"Just saying."

"Hmph, there will be no express if the island is destroyed." Shadow glared at the big blue engine.

"Well let's not think about the negatives." Sonic said.

Shadow shook his head and turned to his blue rival.

"That's just like you Sonic, you always think everything's gonna be alright. News flash, nothing is going right! It'll take more than a few taunts, laughs and more annoyances like you to fix all of this." Shadow growled.

"Hey lay off Shadow, we always get the job done...and whatever happens I WILL take care of it, all of us together." Sonic waved to the others.

"What's your problem Shadow!" Shade growled.

Before Shadow could say anything Sonic butted in.

"Sorry Shade, Shadow is just a grouchy fake who couldn't handle the fact the a fake Biolizard came to destroy the island, just to get blasted by whoever that was who hit him." Sonic teased.

"SHUT UP FAKER!" Shadow roared at him.

"I figured Shadow would know who that guy was...he looked like him only crystalized!" Tails said.

"Well I don't...I don't have a clue!" Shadow turned to him.

"Well he may know YOU!" Percy added.

"Hmph as if. I bet I could find whoever did this and make them pay. No doubt they were the ones who brought the Biolizard back.

"You won't be able to do this alone Shadow." Sonic warned.

"YOU CALLING ME WEAK?" Shadow growled.

"NO I'M CALLING YOU INSANE!" Sonic shot back.

Big decided to interrupt making a rather BIG mistake.

"Um...guys shouldn't we be talking about-"

"SHUT UP YOU OVERGROWN FURBALL!" Shadow roared.

This took everyone by surprise...Shadow even just registered what he said...but then he went with it.

"SHADOW!" Sonic yelled.

"Why are you insulting me?" Big asked.

"THIS IS PROBABLY YOUR FAULT TO BEGIN WITH! MAYBE YOU HAVE SOMETHING TO DO WITH IT!" Shadow pointed at him.

"But...I..."

"Shadow why would Big do anything bad? He's a very nice guy!" Shade argued.

"Hmph...he's nothing but trouble!" Shadow crossed his arms.

Everyone watched as Big shut his eyes tightly and clenched his fists. Tears started to form and he let out a large wail. He ran off down the line crying before anyone could stop him.

"BIG WAIT!" Tails yelled.

But he was already gone, the engines watched in horror at what Shadow had done.

"What gives you the right to say things like that?" Edward asked.

"Oh don't get me started on you engines, especially YOU THOMAS!" Shadow pointed at him.

Thomas looked between his friends and back at Shadow.

"What?" Thomas asked.

"You're hiding something...what were these buffers so important about, those buffers out of all the others on this damn island!" Shadow said.

Sir Topham Hatt went to interrupt.

"Shadow I do not allow profanity around-"

Shadow gave him a deadly glare and STH backed away.

"Shadow there are just some things we'd rather not talk about...especially something that's more personal to me." Thomas said.

"JUST TELL US ALREADY!" Shadow roared.

"NO!" Thomas yelled back.

This took everyone by surprise...even Shadow. Sonic, Tails and Shade look back at each other. The engines knew Thomas was right not to tell...what laid around those buffers was something secretly remembered all to well...and often chatted about it. Even Thomas chatted with the toned down Diesel 10 who had given up on that plan long ago after his little accident. Thomas protected those buffers the most though...especially since they were an access to someone very special to him. And he wasn't going to let anyone touch them.

"Sonic is it that serious?" Tails asked.

"Yes...it is." Thomas sighed.

Sonic, Tails and Shade now understood...some secrets needed to be kept hidden...for now. But Shadow was having none of it and stepped in front of Thomas.

"Thomas...don't make me force you tell us what you're hiding. I bet those buffers are nothing special at all...probably just your favorite spot to-"

What happened immediately was something that engines and mobians would never forget. Thomas angrily raced up and his buffer crashed into Shadow's face knocking him down. Thomas said nothing and raced down the line. The engines, STH, Sonic, Tails and Shade were in complete silent horror. They had never seen Thomas so angry...or actually attack one of the mobians like that. Their shock was interrupted by Shadow groaning

"Ugh...that actually hurt." Shadow rubbed his face.

Suddenly Shade walked over and just as Shadow got up, Shade sucker-punches back down before punching him 3 more times and Sonic had to race over and hold her back.

"SHADE STOP! THAT'S ENOUGH!" Sonic said.

"YOU ASSHOLE! DON'T YOU EVER TALK TO THOMAS OR BIG LIKE THAT AGAIN! YOU'RE LUCKY METAL SONIC ISN'T HERE OR HE WOULD'VE KILLED YOU!" Shade snarled.

Shadow groaned and could smell his own blood that was smeared across his face. STH decided to close the meeting quickly.

"Uh...you all better find somewhere else to sleep. And we'll hope for the best tomorrow." STH said.

The engines groaned again before whistling goodnight to Sonic, Tails and Shade...but no one said goodnight to Shadow. Gordon, Henry and James just wheeshed him.

"Better him than me." Edward smirked.

"I hope Thomas and Big are okay." Percy said.

"Come on, let's go find them again." Shade said.

"Hey Sonic...you think more clones will start appearing?" Tails asked.

"I don't know Tails, but we must find the source of this cloning. If Shadow wants to do this on his own, then fine...but we're sticking together." Sonic said.

Shadow had been left alone and in his thoughts. He stood there wiping the blood from his face and he noticed he was now alone.

"Hmph...guess I did screw up...no matter...I will do this on my own. But a clone of me? Someone who may possibly have my powers...who could that be?" Shadow wondered.

Meanwhile by the buffers, Big had found a troublesome truck to rest in and was crying. Froggy just laid next to him as comfort. He was very upset by Shadow's words.

"I'm...I'm only trying to help. Why did he say all that?" Big cried.

While he was crying...he didn't hear someone coming close to him. Thomas was on his way over still fuming over Shadow's attitude. He honestly didn't care how anyone reacted to what he did, he just needed to get some air. Unfortunately as he came towards the buffers, he forgot how fast he was going and put on his brakes. He could see a truck in the way of the buffers now and Big was just sitting up.

"Huh?"

"OH NO!"

Thomas tried to stop, but then there was trouble. He slammed into the truck and Big screamed as he rolled towards the buffers. Suddenly a rainbow-colored portal opened up right in front of the buffers and Big disappeared right through. Thomas stopped just as the portal closed.

"Uh-oh...now what will I do?" Thomas gasped.

Hiding nearbye, the crystalized hedgehog hummed.

"So that's how it works...and it seems this engine may have some connection with those emeralds...interesting...but the danger is far from over!" He said.

 _ **End of ARC 3.**_

 _ **To be continued in ARC 4: Titans of Sodor...**_


	6. Chaos PT 1

ARC 4: Titans Of Sodor

Chapter 6: Chaos PT 1

The Steam Team remained upset and angry as they were forced to sleep in different places, it reminded them of when they had accused the diesels of ruining the sheds long ago. Luckily for Toby he got to go back to his shed. Emily went back to her older shed, Gordon slept at Knapford station, James slept at the docks. Edward and Henry had to sleep in the Steamworks plus they needed repairs. Percy and Shade headed off to the Smelter's Yard, though they were wondering where Thomas and Big had run off to. Percy was still surprised at how Thomas attacked Shadow, though he did deserve it...but still. Percy still had chills when coming near the Smelter's Yard after what had happened last year.

"Ooh, I wonder if Thomas is okay. Maybe I should go look for him." Percy figured.

Shade yawned from inside the cab and stretched.

"I'm sure wherever he is he's fine, it's best to worry about it tomorrow and hope we figure out who's causing all this." Shade said.

"I guess so...oh dear."

Meanwhile, Thomas was panicking over by the buffers. He worried if Big was okay, he could possibly get lost there. He knew he'd eventually have to tell Sonic and the others what happened. He thought about heading in after him, but there was nothing beyond the buffers that could really harm him, if anything, what was hidden would keep him protected. Besides, he had no idea where Sonic had gone, so it would be useless to tell him now. And so Thomas left to find some other place to sleep.

 **The Magic Railroad...**

Big had abandoned the freight car and was now floating down the long stretch of track admiring the night sky of this strange little world. It looked a bit like Sodor, it's beautiful mountains, it's light green grass, and the twinkling stars.

"Ooh...it's so pretty." Big said.

Froggy remained on his shoulder as they continued to float down the golden rails.

"I wonder where I'm going." Big said.

"Ribbit!" Froggy said.

Eventually they were coming closer to another set of buffers. Their floating speed picked up and they started to wobble.

"Whoa...wait it's the end of the line, what happening? HANG ON FROGGY!"

Big and Froggy zip into the portal created by the buffers and they were gone again. A few seconds later they exited out another set and into a large tunnel. Big landed on his butt while Froggy landed next to him.

"Oof! Owie...hey where are we now, it's too dark." Big said.

Nervously, he walked forwards and could see something in the distance with dimmed lights. Exiting the tunnel, he saw what looked like an engine a bit smaller than Thomas...it seemed asleep. Or so he thought. Big gasped when the engine woke up and looked at him with a smile.

"Oh hello there."

 **Island of Sodor...**

The next day, the island was being visited by a special guest, Sonic and Tails never thought they would ever see these two again. With Gordon sleeping at Knapford Station, he knew he'd be ready for the express, though he had to wait until either Thomas or Percy fetched his coaches.

"I wonder who this famous celebrity is." Gordon wondered.

Emily arrived yawning next to him.

"Ooh, I heard about him, he made this movie with these little alien things called Chao. I think the movie was called 'Planet of the Chaos'. It sounds very interesting, he and his assistant are coming, maybe they'll be on your express!" Emily said.

"Well I'll be sure to give them a good run. Though those little ghosts may become a bother...they'll probably try to scare him away." Gordon rolled his eyes.

"I'm sure they won't do that, just keep a lookout for him." Emily said.

She steamed away while Percy came over shunting Gordon's coaches and pushing them into the back of Gordon. Percy then moved beside Gordon and came up to him.

"Gordon, have you seen Thomas? I can't find him, nobody can." Percy said.

"No I haven't seen him, I've been here all night thanks to the large lizard destroying the sheds. I hope they get fixed soon." Gordon grumbled.

"Yeah me too, I'm gonna continue to find Thomas." Percy left.

Percy thought about checking where the magic buffers were, surely Thomas had to have gone there...he just hoped whoever they saw trying to attack them wasn't around. Unfortunately he was wrong, the crystalized hedgehog spied on Percy as he headed towards the buffers.

"Hmm...what is this engine up to?" The hedgehog wondered.

Before Percy could even get close to area the buffers were located in, a small alien ship goes flying by seemingly out of control.

"Whoa...who could that be?" Percy wondered.

So instead Percy abandons his mission and decides to follow the ship down another set of track, unknowingly angering the hedgehog. Meanwhile, Shade found Sonic standing on a large hill by the Windmill. He looked puzzled and angered at the same time.

"Something troubling you Sonic?" Shade asked.

"I'm just still angry over how Shadow treated everybody, they didn't deserve that, and thanks to him we can't even find Big...or Thomas." Sonic sighed.

"Is Shadow always this mean?"

"No, he can be a jerk...but he's never this...grumpy I guess. Heh, probably just jealous we could handle the Biolizard without him, not like he remembers much from the first time."

"I guess so. Hey Sir Topham Hatt said that some celebrity is supposed to be coming in an hour, Tails said you all might know him."

"A celebrity eh? I don't know many of those...guess I'll be surprised." Sonic smirked.

"Hello Sonic!" Came a voice.

Sonic and Shade nearly jumped in shock, but as they turned around, Sonic smirked recognizing the person.

"Heh...didn't expect to see you here again." Sonic chuckled.

All around Sodor, many were wondering who the famous person was, not many have about the movie, but soon they were sure to learn all about it. Back with Percy, he continued to follow the ship, it looked very similar to one of the Metarex ships. Finally the ship crashes into the side of the Steamworks. Luckily no one was hurt, though Victor and Kevin quickly come out to see what was going on, some workmen were a little scared when they saw the ship. Percy arrived a little worried.

"Is everyone alright?" Percy asked.

"Just fine Percy, but whatever is this thing?" Victor asked.

"I don't know, I was following it down the line, it seemed out of control." Percy said.

Suddenly everyone backed away as the top opened up and inside was in fact one of the Metarex, not any of the commanders however, instead it was the insane Metarex Kingape, the Metarex that looked like a monkey.

"Ugh...I really need to work on better landings." The metarex rubbed his head.

"Oh no! We're being attacked by the Metarex again!" Percy gasped.

"We need to get Sonic!" Kevin said.

"Defend the Steamworks!" Victor yelled.

Several brave workmen gathered crowbars and hammers and went to attack the mech who began to panic.

"WAIT WAIT! I'M NOT HERE FOR AN ATTACK! STOP IT! STOP!" Kingape clutched his head.

"Then what could you possibly be here for?" Percy asked letting off steam angrily.

"Our leader has gone missing and his signal was traced back down here, figures, I can understand aliens on this planet, but to end up on this Island again? Why?" Kingape wondered.

"Wait so only Dark Oak is missing?" Kevin asked.

"Yeah the other 4 sent me down here to look for him, apparently he could be very hurt. When I find him, the others will come to get him." Kingape explained.

"But how did he end up here?" Percy wonderred.

"That's what I'll find out when I find him. But now there's a new problem, my ship is totaled and I'm sure no human could fix it." Kingape gestured to the workmen who scoffed.

"Hmm, maybe Tails will know what to do. Look you can come with me and we'll go get Tails, maybe we'll run into Dark Oak along the way. As long as it's not literal." Percy remembered the deaths of Captain Whiskers and Johnny.

Kingape scratched under his head with his sharp claws, could he really trust these sentient machines...then again...they were kinda connected after all, well if you ignore that fact that Dark Oak and the commanders were once plant-like aliens now fused into bio-robotic forms. But besides that, they were all machines now.

"Very well..take me to this Tails you speak of." The Kingape said.

He jumped into the cab nearly knocking over the driver and fireman. Kingape himself nearly hit his head on the roof.

"Ugh...at least you're not any smaller." Kingape groaned.

Percy only chuckled before leaving to find Tails at Sir Topham Hatt's house. The fox was being informed by the fat controller of the special guest.

"Whoa...so he's actually coming. It's been awhile since we've seen him, just hope he's doing well for himself." Tails said.

"I heard his next movie is almost finished. He wants the last scene to take place here on the island, as sort of a peaceful ending." STH explained.

"Oh...he may have a hard time with that." Tails said.

"Well, we need to figure out who's causing all of this trouble." STH said.

"Don't worry sir, me, Sonic and Shade will handle this mess. I don't know where Shadow went off to, that guy can be so mysterious, and we still haven't found Big." Tails said.

Suddenly Percy arrived with Kingape who was admiring the view.

"So why do you call him the fat controller?" Kingape asked.

The driver and fireman felt uncomfortable explaining that and Percy thought it was pretty obvious why. Tails, STH and Lady Hatt came out greeting Percy.

"Hey Percy...AAHH A METAREX!" Tails shouted.

"I'M NOT HERE TO FIGHT! Ugh...I'll have to explain this to everybody." Kingape groaned.

"Tails, Kingape's ship is ruined and I thought maybe you can fix it. Apparently Dark Oak got sent here by some unknown source and now he's missing, so he needs to find him." Percy explained.

"Wow...now that is strange. Well I guess I could take a look at it. Where did you crash it?"

"The Steamworks."

Back with Sonic, he and Shade were still staring down the unexpected person.

"So what's the deal Metal?" Sonic asked.

He and Metal Sonic just stood there inches apart staring at each other. Knowing they were unable to tell how he was feeling, he simply stood there with sharp claws clenched into fists at his sides.

"I'm just here for a visit...what brings you here Sonic?" Metal asked.

"Saving the island again, though now I'm thinking you have something to do with everything that has been happening." Sonic accused him.

"Hah...I don't even know what's been happening. I just got here." Metal Sonic said.

"Sure you did. You're working with that strange crystalized hedgehog we saw yesterday aren't you! I thought you were done working for people." Sonic said.

"I don't know what the hell you're talking about." Metal growled.

"JUST FESS UP!"

"SHUT UP!"

Shade could sense the strong tension between them and was thinking about breaking it up, suddenly they are joined by another person.

"Wow Sonic...you really do know how to cause tension, this is perfect!" Came a familiar voice.

The three turn to see a female echidna holding a video camera. Sonic blinked a few times trying to register who he was seeing.

"Tikal? Is that you?" Sonic asked.

"Hi Sonic, long time no see. How are you?" Tikal asked.

"I'm doing great Tikal, how's Chaos?" Sonic asked.

Suddenly the large blue ex-enemy Chaos 0 came over wearing some sunglasses, he only nods to Sonic.

"Chaos! Hey wait...but I thought you were one with the Master Emerald." Sonic said.

"We found ways to still maintain physical forms, plus Chaos even managed to become popular enough to be given a movie deal. Surely you've heard of 'Planet of the Chao'." Tikal said.

"Yeah, but I didn't get to see since Egghead constantly attacked. Meaning I didnt know Chaos had became a celebrity." Sonic shrugged.

"Huh...even I missed it." Shade said.

"You had a movie?" Metal tilted his head.

Chaos nodded and Tikal had to speak for him.

"So did we interrupt something?" Tikal asked.

Sonic and Metal turned back to each other.

"Sonic...I'm only here to visit, but if the island is in danger again...then I'll help." Metal said.

Sonic and Metal continued to stare at each other for another minute. Shade, Tikal and Chaos watched worried about what was going to happen. Metal figured if he was gonna have to fight Sonic over this, he'd gladly do it. But thankfully, Sonic backed off.

"Heh, I guess you've really softened up." Sonic teased.

"ME? NEVER! NOT FOR YOU!" Metal growled.

"Keep thinking that." Sonic said.

Seeing he had ticked off the robot, Sonic raced off with an enraged Metal right behind him. The girls laughed while Chaos only adjusted his sunglasses.

"So I heard you're looking to do some film-making here right?" Shade asked.

"Yes." Tikal nodded.

"Maybe I can help with that."

Nearbye, the crystalized hedgehog evilly laughed.

"So they're trying to make another film huh? I'll give them the footage that they so desperately want." He growled.

By the docks...something was rumbling in the water causing a few large waves to come crashing into Cranky who was getting worried.

"What's going on in the water?" Cranky wondered.

Salty and Edward looked towards the water seeing more rushing waves.

"I don't know matey, but maybe we should shut down the docks until it settles." Salty figured.

"It would be the best option." Edward agreed.

While the worry continued at the docks, Percy had dropped off Tails and Kingape back at the Steamworks where Tails went to work on the ship. Percy noticed someone standing far in the distance and squinted his eyes.

"Huh? Who's that?" Percy wondered.

Then he saw the person motion him to come over, Percy was very skeptical.

"I don't know if I should go, could be some kind of trick." Percy said.

He shuts his eyes tightly for a few seconds, and when he reopens them, the figure was gone.

"Phew, maybe I was just imagining things." Percy smiled.

"Oh I wouldn't be so sure." Came a voice.

Percy's eyes widened and he looked around, no one was there.

"Who's there?" Percy asked.

But he got no answer, so he instinctively raced away and hid in a nearby single shed. He hoped whoever it was would go away.

"I think I'm safe." Percy whispered.

"I don't think so."

Percy suddenly found his eyes forced shut, then when he gets to reopen them, he was staring into blood red eyes with yellow pupils and a black slit in the middle of them.

"AAAAHHHHHH!" Percy screamed backing up.

With one clawed hand, the hedgehog swiped the air and the force knocked Percy into the back of the shed. Percy saw it was the same crystalized Hedgehog from before.

"You...why are you here? What do you want?" Percy asked.

"I am...Mephiles the Dark."

 _ **To be continued...**_


	7. Chaos PT 2

Chapter 7: Chaos PT 2

Percy gasped, he knew this hedgehog was someone he should never mess with. The hedgehog hung his head down seemingly staring at the ground, then he walked like a zombie towards Percy.

"You engines are much more determined than I thought...I find it very interesting. But I know you'll all be easy to take out, oh yes." Mephiles said.

Percy could say nothing as Mephiles continued to walk towards him, his gloved claws scratching Percy's lamp. Percy didn't know whether to yell or race forward...he could only stay still, his driver and fireman had ran off in fear. After a few more moments of silence, Mephiles lifted his head up to stare into Percy's eyes.

"Your friends are doomed...they will never win. Last year was only luck...but you'll go down just like the others. How cruel the inevitable is..." Mephiles purred.

He tilted his head as Percy's eyes stay locked on to his own. Finally Percy gained the courage to speak.

"Why? Why are you doing this?" Percy asked.

"Oh just because I love the effects of chaos and destruction...I crave it...and I will do it all. That blue hedgehog will not defeat me...and I figured going after his newest allies would help him see how he's on the losing team. That blue engine will be of some great use to me...and I know you all are holding info from me about what's beyond those buffers. Something that keeps this island alive...keeps people coming...KEEPS YOU WINNING!" Mephiles growled.

"NO!" Percy shouted.

Percy backed up a bit letting off steam.

"GIVE IT UP!" Mephiles floated into the air.

"LEAVE ME ALONE!" Percy yelled.

He chose to race forward and thankfully miss a orb that was shot from Mephiles' hand. Mephiles chased Percy down another line away from the Steamworks.

"YES! RUN! RUN YOU LITTLE GREEN PEST!" Mephiles shouted.

He continued to fire shots around Percy instead of directly hitting him. Percy screamed and whistled as he moved onto different points and sped faster and faster. No other engines were around though Percy figured he would run into Gordon since he was on the main line. Mephiles flew closer and scratched his claws across Percy's side.

"OOOWWW!" Percy winced.

Percy was hoping Sonic or one of the others were around, but unfortunately they weren't. Some trucks were sitting in a siding and the points were switched to it.

"Oh no!" Percy gasped.

Mephiles then shoots an orb at the trucks blowing them up and the force knocks Percy off the rails and he slides down a bank. Mephiles loses sight of him as Percy disappears under a lot of trees. Percy clipped a few of them and loss control swerving around, hitting rocks and finally bouncing off a ledge. Nearby, Sonic and Metal were still racing around when they spotted Percy go flying from one ledge, over a pair of tracks and down another bank.

"Whoa...how the hell did that happen?" Sonic asked.

Metal detected someone else coming and waited for it. When it was time, Metal raced forwards and managed to tackle Mephiles onto the ground hard creating a large cloud of dust. Sonic winced and remembered Percy was in trouble.

"METAL, I'LL GET PERCY! YOU STOP WHOEVER THAT IS!" Sonic called out.

Without waiting for an answer, Sonic took off down the bank to catch up with Percy who was still sliding down. Sonic raced in front of him and Percy was happy to see the blue blur.

"SONIC!" Percy yelled.

"HOLD ON PERCY!"

Sonic could see another small ledge up ahead and below were tracks. Sonic then gathered up his strength and spindashed into Percy's side knocking the small engine a bit into the air and landing right next to the tracks.

"Barely made it." Sonic sighed.

Paxton was coming by with some trucks and just saw the last of the action, he stopped confused.

"Oh my...what just happened?" Paxton asked.

"Um...it's a long story. Which reminds me, I need to make sure Metal is okay...wow...I never thought I'd say that." Sonic shrugged.

"I'll go get Rocky." Paxton said.

"Thanks Paxton!" Percy said.

Meanwhile, Metal and Mephiles were duking it out in the sky as they raced around. They were currently grappling with each other trying to push the other away. They spiraled around the sky in a streak of blue and purple.

"UGH! LET GO OF ME YOU SCRAPHEAP!" Mephiles growled.

"NOT UNTIL YOU LEAVE THIS ISLAND!" Metal growled back.

Sonic followed the streaks but is suddenly sidetracked when the ground below him starts to rumble. He could hear people screaming in the distance.

"HELP! THERE'S SOMETHING IN THE WATER!"

"HELP! IT'S A GIANT MONSTER!"

"RRRRRROOOOOOOOOOOOOOAAAAAAAAAAAAAAAAAARRRRRRRRRRRRRRRRR!"

Sonic recognized that roar...but something didn't seem right...he needed to get to the docks quick. At the docks it was complete chaos...literally. All the engines and workmen had evacuated, except for poor Cranky who had ended up knocked down. There in the distance of the water...was a clone of Perfect Chaos, it had a purple glow around it...meaning it was created by Mephiles. Perfect Chaos had shot one of it's water tentacles and knocked Cranky down. Sonic arrived at the docks and looked horrified.

"No...it can't be. But it's just a clone, Chaos has no reason to absorb the negative power of the chaos emeralds anymore." Sonic said.

Perfect Chaos seemed to notice Sonic and roar at him.

"YOU'RE GOING DOWN AGAIN!" Sonic promised.

Suddenly Shade teleported beside him.

"Whoa...hey that looks like Chaos. But he's with Tikal." Shade said.

"Where are they?"

"I gave them a map of good places to film the rest of their movie, and I heard the roar so I came to help." Shade said.

"No need, I've defeated this guy twice already! I already know how to defeat him!" Sonic smirked.

"He could try something new this time though." Shade warned.

"We'll just see about that." Sonic adjusted his gloves.

"Hmm...Sonic have you seen Thomas lately?"

"Strangely no...I'm getting a little worried." Sonic said.

"Well I'll go look for him." Shade said.

After Shade teleported away, Sonic went into action knowing he needed to boost into the bottom of Perfect Chaos's body and spiral up through his head, but of course along the way he would have to dodge any blasts Perfect Chaos threw at him. Meanwhile, Metal and Mephiles found their way to Knapford Station where everyone had ran off after the two ended up destroying the station during their brawl. Metal had thrown Mephiles into a support beam and the hedgehog did it back.

"I'LL END YOU HERE!" Mephiles growled.

"AS IF!" Metal scratched under his nose.

Mephiles sent some orbs towards Metal who dodged them and they damaged more of the station and broke all the windows. As they kept fighting, they failed to notice Toby who was just coming by.

"Oh my...the station is destroyed." Toby gasped.

Then he saw Metal and Mephiles looking right at him.

"Do you mind?" Mephiles growled.

"Kinda busy here!" Metal groaned.

Toby says nothing and quickly leaves the awkward moment. Once he's gone, Metal tackles Mephiles back into the sky and they go flying towards the Smelter's Yard. Mephiles grabs Metal and makes him break his fall as they hit the rails hard. Metal got up seeing he was still fully intact. Mephiles floated up onto his feet laughing evilly.

"HAHAHAHAHAAAAAAA! You fool, I cannot be so easily defeated. I'm immortal after all...it'll take more than you to defeat me. I will discover what keeps this island alive and I will destroy it...you won't stand in my way." Mephiles vowed.

"I'll fight you until I run out of power...and I'm nowhere near that." Metal said.

"You're strong I'll give you that...but I'll still win. I don't even need my powers to beat you!" Mephiles growled.

Metal flexed his claws and balled them into fists.

"Bring it on." Metal said.

Mephiles raced at Metal and punched him in the face almost hard enough to make a dent, Metal only skidded back a bit. Metal retaliated by punching Mephiles in the gut, only for the evil being to head-butt the robot. Metal lunged back to claw him in the but Mephiles grabbed his arm and threw him on the ground. Metal jumped back up and back-handed Mephiles away.

"That all ya got?" Mephiles laughed.

"You're about to find out!" Metal growled.

The two lunge at each other. Meanwhile, Tikal had sensed a strange energy near one of the sidings and she and Chaos were following it. They had ended up by the magic buffers and Tikal touched them.

"The energy is here...I can feel it, it's really strong. But what's causing it?" Tikal wondered.

Suddenly they hear a rumble, the sound of an engine coming from behind. They turn to see Thomas looking at them confused and cautious. Tikal gasped and Chaos instinctively got in front of her making Thomas back up a bit.

"Wait Chaos...this engine...I can feel the same energy from those buffers...on him." Tikal said.

Chaos backed off and Tikal went to touch Thomas' front deck. She closed her eyes and smiled.

"I sense good in you...lots of it. Are you the guardian of these buffers?" Tikal pointed to them.

"I guess you could say that...whoever that crystal hedgehog is...I can't let him get near them again. My name is Thomas." Thomas said.

Chaos nodded in respect, he even removed his sunglasses. Tikal sighed and smiled bigger.

"My name is Tikal and this is Chaos. Thomas, you can't do this alone, I know you care deeply for the hidden secrets within them...but I fear if you don't require help...it may be too late." Tikal said.

Thomas looked down in shame, he should've been able to trust Sonic enough to tell him the secrets...but what if the enemy was listening? He bit his bottom lip and let off some steam.

"But what if...if..."

"Thomas...please...I know danger is approaching. If anything, the help you truly seek may come from beyond those buffers. You need to be able to tell Sonic and his friends." Tikal said.

Thomas knew she was right...and it was best to find them now.

"Okay...I will..." Thomas smiled.

Unknown to them...a certain black hedgehog was listening in on them as Thomas began to reveal what the buffers truly led to. Needless to say he was very surprised.

"Hmph...magical engine?"

Back with Sonic, he had successfully damaged Perfect Chaos twice and he was tiring out. Perfect Chaos had managed to hit him a few times with it's water tentacles and energy projectiles. But Sonic had pressed through with Cranky and people nearby cheering for him. Sonic raced off the dock and boosted across the water as one of the water tentacles raced at him. Sonic leaped up high and gets smacked upwards.

"HAH! THANKS FOR THE LIFT!" Sonic yelled.

He spindashed into the watery brain of Perfect Chaos one last time and the sudden impact blew it up.

 **"RRRRRRRRRRAAAAAAAAAAAAAAAAAAAAAAAWWWWWWWWWWWWWWWWWRRRRRRRRRRRRRRRRRRRRRR!"**

In an instant, Perfect Chaos was destroyed, though the explosion of water poured onto the docks flooding it for a few seconds drenching Cranky.

"Ugh...bleh!" Cranky said.

Sonic laughed as Cranky spit out some water. Several water drops exploded into purple particles that faded away.

"Ugh...I hope that's the end of those clones." Sonic said.

Now he worried if Metal was doing alright, he needed to get back to him quickly. Back at the Smelter's Yard, Metal was losing the fight, no matter how hard he fought back, Mephiles would not go down. His systems were winding down as Mephiles kept punching him.

"YOU WEAK USLESS RUSTBUCKET! YOU DON'T STAND A CHANCE!" Mephiles punched him again.

Metal staggered towards the back of the building where the melting pit was. Metal managed to punch Mephiles 4 more times before Mephiles tackled him and pummeled him in the face. After a few seconds he dragged Metal to the edge of the track and held him above the melting pit.

"It's been a good fight...but you bore me." Mephiles said.

But before he could drop him, Mephiles is rammed into knocking him away and the saver grabs Metal and the two teleport away. Mephiles gets up seeing he was alone.

"UGH! NO MATTER...I STILL GOT SOME SURPRISES FOR THEM! I'LL DESTROY THIS DAMN ISLAND...AND TAKE THE POWER THOSE ENGINES ARE HIDING WITH ME!" Mephiles promised.

He flew out of the Smelter's Yard figuring out his next plan. Back at the Steamworks, Tails had finished working on Kingape's ship, and when he finished, the radar popped on showing Dark Oak's location. Kingape gasped and started hopping around and clapping like a real monkey.

"I FOUND HIM! I FOUND HIM! I'M COMING MASTER!" Kingape cheered.

The signal wasn't that far away. Kingape and Tails raced over to a small wooded area near the Steamworks and saw something sparking. They discover the body of Dark Oak, he was just waking up too.

"MASTER?" Kingape said.

Dark Oak sat up and looked at them.

"What happened?" He asked.

"You were passed out sir, the others sent for me to find you and then let them know." Kingape said.

Dark Oak noticed Tails and immediately stood up.

"YOU! I DON'T NEED YOU AND THAT ANNOYING HEDGEHOG GETTING IN MY WAY!" Dark Oak growled.

"We're not, we're trying to-"

"I DON'T CARE! Now then...I'm getting out of here...I don't know who decided I should be sent back here, BUT WHEN I FIND OUT WHO DID IT I'LL-"

Suddenly, some red orbs come towards them and they all dodge.

"Who threw that?" Tails wondered.

Looking out into the clearing...he gasped when he saw a familiar evil knight looking right at him.

"WHAT? KING ARTHUR? BUT WE KILLED YOU!" Tails shouted.

Kingape and Dark Oak came out into the clearing as well. King Arthur swung his sword threateningly...strangely he was missing his scabbard.

"Indeed you did...but I've been revived by him!"

King Arthur pointed a claw to Mephiles who stood nearby chuckling, then he vanished. Tails realized that hedgehog may be the cause of everything.

"AAHH! WHO IS HE?" Kingape gasped.

"HE MUST BE THE ONE WHO SENT ME HERE IN THE FIRST PLACE!" Dark Oak growled.

He took out his own sword threateningly. King Arthur laughed.

"Hah...you think that sword could hurt me?"

"YOU'RE GONNA FIND OUT VERY SOON!"

"CHALLENGE ACCEPTED!"

Dark Oak and King Arthur immediately get into a swordfight while Tails and Kingape face-palm.

"Um...what now?" Tails asked.

"I need to contact the other commanders..." Kingape raced to his ship.

"Well I need to contact Sonic. If we're going to defeat that hedgehog and save this island...and possibly you all...we all need to work together...we could use all the help we can get." Tails said.

Kingape turned to him and crossed his arms.

"Like the Metarex would help our enemies...besides we have nothing to do with this. Especially me, I don't like to fight, I'm more of the trapping kind." Kingape said.

"Oh come on, don't you want to prove to Dark Oak that you can be pretty tough in combat too?" Tails asked.

Kingape realized he had a point...he was always a coward...maybe it was time to step it up. Tails held out a hand.

"Truce...until this is all over..." Tails said.

Kingape hesitated at first...but gave in eventually. He flexed his sharp claws then shook Tails' hand.

"Deal."

 _ **To be continued...**_


	8. Chaos PT 3

Chapter 8: Chaos PT 3

While Kingape went to contact the other Metarex commanders, Tails tried to get the fight between Dark Oak and King Arthur under control, plus he needed to find a way to defeat King Arthur yet again. He seemed a lot more powerful now, able to block most of Dark Oak's swipes. Dark Oak angrily swiped wildly at the ex-king who dodged it and tried to stab Oak in his large green eye but the Metarex jumped back before lunging again and kicking the knight onto the ground.

"YOU'LL NEVER WIN! AND I WILL DESTROY YOU ALL!" Dark Oak roared.

Tails flew over and grabbed Dark Oak's shoulders to hold him back.

"You need to calm down Dark Oak, we need to think of a better strategy! From what Sonic has told me, he is very powerful and you need to be quick. I don't know if your sword is truly powerful than his." Tails warned.

"I KNOW IT IS! GET OFF ME YOU YELLOW PESK!" Dark Oak growled.

He yanked Tails off and threw him to the ground narrowly dodging King Arthur's next swing.

"Ugh...yep he's about as stubborn as Sonic." Tails chuckled.

Before Tails could attempt again, Dark Oak finally managed to strike King Arthur and the ex-king goes flying right through the wall of the Steamworks. Victor and Kevin quickly flee the building as Dark Oak charges in and he and the knight brawl all around the Steamworks. Tails goes over to Kingape's ship where the monkey metarex is still trying to contact the commanders.

"Any luck?" Tails asked.

"Almost got it!" Kingape said typing rapidly.

Finally four large screens popped up revealing the other four commanders Pale Bayleaf, Black Narcissus, Red Pine and Yellow Zelkova. Tails felt it was too late to hide now, then again, he needed to try to at least get them to cooperate.

"Metarex Kingape, have you found our lord?" Pale Bayleaf asked.

"Yes I have...he's been sent back to this island you guys try to invade last year." Kingape said.

"Ugh...that place again?" Red Pine face-palmed.

"For what reason?" Black Narcissus rubbed under his chin.

Finally Tails cleared his throat loudly getting their attention turned on him.

"YOU!" They all shouted.

"Listen, I can explain at least some of what's going on." Tails held up his hands.

"Let me guess, you found a way to kidnap him?" Yellow Zelkova guessed.

The others look at him and groan.

"Why would he do that?" Pine argued.

"I don't know...just guessing." Zelkova turned around crossing his arms.

Tails continued.

"I believe this new strange hedgehog named Mephiles has been making clones and reviving old enemies from our past. I assumed he managed to find and kidnap Dark Oak to control him and make him destroy the island...but I guess he fought the control but got damaged in the process." Tails explained.

"Dark Oak is one of the strongest beings in the galaxy, no mind control could possibly work on him, not even us." Narcissus scoffed.

"It looks like it." Tails sighed.

"Well where is he now, we need to speak to him." Bayleaf said.

"He's currently fighting with one of the past villains...actually...I still haven't figured out why, it's Mephiles we need to lookout for." Tails said.

"We don't want part of any of this crap you and that blue menace are doing. It's none of our business." Pine growled.

"I like to fight...but this is a waste of time." Zelkova said.

"Finally we agree on something." Pine said.

Before anything else could be said, the door to the ship is blasted off and in comes Dark Oak slamming into a wall. Then comes King Arthur who's eyes are glowing purple.

"Hah, you really need to work on your swordsmanship. It's pathetic...like yourself." King Arthur laughed.

Everyone noticed Dark Oak looked more damaged, he was on one knee and gripping his sword tightly. His other hand was on the ground, his long sharp claws digging lines, and his head hung down.

"I can't lose to someone like you...the Metarex never lose. WE CAN'T LOSE...NEVER!" Dark Oak roared.

In a flash he stands up and dashes at King Arthur in a blur of purple, King Arthur had no time to react when Oak slams his fist hard into his head knocking the ex-king into another wall. Seconds later he started to flicker away.

"WHAT? NO! WHAT'S HAPPENING TO ME?" King Arthur yelled.

Suddenly he flashes away, and replacing him was Mephiles who started to evilly laugh.

"Hah...that was only a distraction! I needed to get you to contact the others just for them to witness what will happen to their precious leader!" Mephiles laughed.

"WHAT?" Dark Oak roared.

He angrily charged Mephiles, only to be blasted back by a purple orb, he hits the wall again struggling to get up. Kingape stayed as far back as he could, but Tails didn't.

"STOP! HE'S HAD ENOUGH!" Tails yelled.

Not thinking, he ran blindly at Mephiles and tried to punch him, but Mephiles blocked his blows.

"Hah, poor kid. Do you really think you have a chance?" Mephiles teased him.

Tails tried to hit him a few more times but Mephiles blocked them all before pushing the fox back. Before Tails could act, Mephiles sucker-punches him to the ground, the Metarex wince all at once. Kingape actually felt sorry for the fox, at least he was trying. Kingape then wanted to at least give it one go, just to prove he had a little bit of bravery.

"I'LL STOP HIM!" Kingape yelled.

"KINGAPE NO!" Tails said.

Kingape lunged at Mephiles, but the dark being actually lets Kingape punch him rapidly knowing he barely feel anything. Kingape swipes his claws a few times but no marks are made. Getting bored, Mephiles sweeps Kingape off his feet before throwing him into the dented wall.

"YOU LEAVE OUR LORD ALONE!" Zelkova yelled.

"And just what are your 4 gonna do about it?" Mephiles challenged.

"WE'RE COMING BACK DOWN THERE!" Pine yelled.

"See ya then fools!" Mephiles waved.

Suddenly he absorbed Dark Oak in a large purple ball and the leader was teleported away.

"NO MASTER!" Kingape yelled.

"MUAHAHAHAHAHAHAHAHA! HA-HAHAHAHAHAHAHAHAHAHAHA!" Mephiles bent his head back laughing.

"FUCK YOU!" Bayleaf yelled.

"WHAT DID YOU DO TO HIM?" Narcissus yelled.

"He's fine with me that's for sure...you'll never see him again...BECAUSE I'LL DESTROY YOU ALL TOO!" Mephiles pointed at them.

Out of rage, Tails tried one last time to hit him, but he only ended up staggering around. Mephiles just walked to him and with one strong punch he knocked him out. Then he turned on Kingape who backed away. The last thing Tails heard was a familiar voice.

CRASH!

"NOT SO FAST MEPHILES!"

"UGH...THAT ANNOYING HEDGEHOG!"

Tails smiled slightly before passing out with one name on his mind.

"Sonic..."

...

...

...

...

"Tails? TAILS? TAILS BUDDY?"

Tails eventually awoke and waited as his vision cleared. Standing over him was Sonic, Metal, Shade and Kingape.

"Tails you okay buddy?" Sonic asked taking a knee.

"Ugh...what happened? How long was I out?" Tails asked.

"About 15 minutes, unfortunately Mephiles got away and the Metarex leaders are on their way here to set up a small base until Dark Oak is retrieved." Shade explained.

"Whoa...that's quite a shiner ya got there." Sonic said.

Tails had a black eye and a bruise on his left cheek, but was mostly okay. Metal Sonic wasn't so familiar with these Metarex, he couldn't trust them. But Sonic, Tails and Shade acted like they weren't a big deal.

"Sonic...are you sure we can trust these Metarex?" Metal asked.

"Well yes...and no. I mean they're evil, but they'll be gone once we find Dark Oak. They wouldn't want to deal with the power of Super Thomas anytime soon." Sonic smirked.

"You say that like they could easily defeat you in super form." Shade said.

Sonic looked embarrassed as all eyes fell on him.

"Well...they can. I guess Thomas just has better control over it then me or Sh-"

"DON'T...bring him up right now." Shade silenced him.

Metal glanced at Kingape, then back at Sonic.

"I don't trust him!" Metal said.

Kingape felt offended and put his claws on his hips.

"How dare you! I'm on your side! I've proven it by trying to defeat that Mephiles guy! Besides I have no interest in destroying anyone." Kingape said.

"Probably because you couldn't." Metal whispered.

"WHAT WAS THAT?" Kingape growled.

Sonic, Tails and Shade backed away. Metal decided to argue.

"You heard me, besides you Metarex probably aren't that fearsome or superier anyway. That title belongs to me, after all I am the superior and real version of Sonic and ultimate robot." Metal bragged.

He glanced to Sonic and his eyes flashed while Sonic only rolled his eyes.

"Last time I checked Metal you were defeated by me every single time we fought." Sonic said.

Metal growled and Kingape laughed at him.

"Ha-ha! That's so sad." Kingape teased.

Metal turned back to the monkey metarex and pointed at him.

"At least I ain't a coward." Metal retorted.

"Well I'm not a pathetic copy of someone."

"YOU'RE ABOUT TO BE SCRAP!"

"NOT IF I SCRAP YOU FIRST!"

Tails decided to intervene.

"Guys come on, can't we just-"

"NO!" They both yell at Tails.

Suddenly Tails, Sonic and Shade race off the ship when Metal and Kingape start brawling. The mobians just stand outside the ship wondering what to do.

"Um...shouldn't we try to break that up?" Shade asked.

"Eh...in a minute, this is starting to get good." Sonic smirked.

Just then they were surprised to see Thomas arrive with Tikal and Chaos in his cab. Stepping off, Tikal and Chaos noticed the robotic rumble inside the ship.

"Um...what's going on?" Tikal asked.

"Nothing important...so did ya find anything interesting for the movie?" Shade asked.

"Oh yes, tons...but we still got some more filming to do so we might be here for awhile. Oh and Thomas is ready to reveal everything." Tikal said.

Everyone turned to Thomas to glanced over to Chaos who nodded.

"Okay Thomas...we need to know everything about that secret, I know keeping secrets is a common thing, but there are also secrets that can help in the future if revealed." Sonic said.

Thomas sighed...but before he could speak, Metal and Kingape came rolling out of the ship in a ball and crashing into the side of Thomas separating them. Shade had enough and activated her leech blades.

"ENOUGH ALREADY! WHAT THOMAS HAS TO SAY IS IMPORTANT SO STOP FOOLING AROUND!" Shade growled.

The two sweat-drop and nodded obediently. Then Percy arrived with several Boos riding in his cab.

"There you are Thomas! Where have you been?" Percy asked.

"I'm sorry for running away Percy, I just needed some time to myself. But I'm ready to reveal the mystery behind the buffers." Thomas said.

Percy understood. And so Thomas began.

"Those buffers lead to a whole other world...and the path to get to it is called the Magic Railroad, it's a mysterious and beautiful place where magic roams endlessly. It connects to a place called Muffle Mountain where my...our...true protector lives. She's an engine...her name is Lady. I met her years ago when Diesel 10 was trying to destroy us all and takeover the island...but he's changed...and I haven't seen her since that one time...except in a dream. I know she would come if the island is truly in danger, but she knew I could do it like last time...and she knew I would have help...which was you guys. But now...if this Mephiles person is as powerful as he seems...then I may have no choice but to call her back again...we need her. She has the power of the gold dust to keep this island alive and could destroy Mephiles." Thomas explained.

Everyone except Percy, Tikal and Chaos were amazed...Tikal just smiled and Chaos nods.

"A magical engine...that's amazing." Tails said.

"Huh...that sounds believable." Metal said.

"I know you miss her Thomas...I assume there was a reason you couldn't visit whenever you wanted to?" Shade asked.

"Before she left, she told me only to come when I truly needed her...though she would give me advice from time to time." Thomas smiled at the few memories.

"I see...well it looks like this may be that time. Hey...didn't Big get sent there then?" Sonic said.

"I believe so...Lady must be taking care of him." Thomas said.

"Good thing too...so Thomas...when are we going to get her?" Percy asked.

"Well...we would need to capture Mephiles first, Lady couldn't do anything if he's not around." Thomas said.

"Hmm...well...we'll have to figure out a plan. Hell for all we know, he could've heard everything just now. But besides stopping him, we need to...oh I can't believe I'm going to say this but...SAVE Dark Oak and King Arthur. And possibly any other people he's probably captured." Sonic sighed.

"Dark Oak won't be happy when all of this is over, at least the other commanders won't worry too much." Kingape said.

"How exactly are we going to find them?" Tails asked.

"The next time Mephiles decides to show up, we'll get some answers. Until then...I say we take a little break. Besides it's best to wait until those other Metarex commanders arrive so they can form a protective barrier around the perimeter. I know we'll finish off this creep together. ARE YOU ALL WITH ME?" Sonic yelled.

He looked to Shade and Tails who nodded, then to Metal and Kingape who dramatically clenched their claws into fists, Chaos and Tikal nod once, the Boos made enthusiastic flips in the air and Thomas and Percy whistled.

"Alright then, we'll show Mephiles just what Team Sonic and the Steam Team can really do!" Sonic said.

"YEAH!" They all cheered.

Later that evening, Pale Bayleaf, Black Narcissus, Red Pine and Yellow Zelkova arrived and manned their chosen spots on the island, all four were heavily armed with Metarex soilders ready to fight against whatever Mephiles had planned. That night, the engines were still upset that they had to sleep in other places. Of course now Victor and Kevin had to find other places to sleep. This time Thomas slept in a large shed where Annie and Clarabel slept. They were worried for him.

"Everything alright Thomas?" Annie asked.

"No...I'm worried about the fate of the island again." Thomas sighed.

"I assume it's much worse then last time." Clarabel said.

"Oh yeah it is, and I'm scared. I need to get to Lady. I told them I'd wait until Mephiles starts to cause trouble again...but it's best to get her before he can find her first." Thomas said.

"Then go Thomas...I'm sure she knows you want to go see her." Annie said.

"I guess you're right. You know, I can always count on you two for comfort." Thomas smiled at them.

Annie and Clarabel blush as Thomas sets off into the night. While he wanted to do this alone, he never knew if Mephiles would try to ambush him along the way. As Thomas stopped to take on water, he sighed.

"I hope Annie and Clarabel were right, I have to do this." Thomas said.

"You're doing the right thing Thomas."

Thomas gasped and saw Sonic, Tails, Shade, Metal, Kingape and an annoying Boo nearby all ready for the experience, Thomas just smiled.

"You didn't think we'd let you do this alone did ya?" Sonic smirked.

A few minutes later Thomas was on his way to the magic buffers and was carrying a freight car behind him holding the mobians, robots and the Boo.

"Is it gonna hurt being teleported this way?" Kingape asked.

"Don't be such a baby!" Metal sneered.

"Why you-"

"Robots." Shade rolled her eyes.

Tikal and Tails laughed while Choas and the Boo shook their head.

"HEY!" Metal and Kingape groaned.

As they moved onto the siding, they could see the buffers straight ahead.

"We're about to go through!" Thomas announced.

But suddenly behind the buffers, the large bushes started to rustle. Thomas screeched to a stop a few feet away from the buffers and everyone looked ahead.

"What's that?" Tails gasped.

Then Shadow comes flying through the bushes and smacks into Thomas' funnel.

"SHADOW!" Everyone gasped.

Shadow groaned and jumped onto the ground.

"LOOK OUT!" He yelled.

Out of the large bushes came a massive blue hulking monster that Sonic remembered all too well. It was bigger than Thomas and looked like a humanoid muscular lizard with gauntlets on his hands, upper arms, feet and lower legs. And he carried a massive warhammer.

"Sonic? You know this guy?" Tails asked.

"Yeah, it's from when I was transformed into a werehog. This is the Dark Guardian, and boy was this guy brutal." Sonic said nervously.

"Wait...it's the real one, so that means it's the real one, so Mephiles might have sent it to guard us from the buffers when he wasn't around." Tails said.

"Uh oh...if Mephiles revived Dark Guardian...you don't think he revived..." Sonic trailed off.

Sonic and Tails looked at each other in horror.

"Oh shit."

"Hmph...I'll handle this on my own." Shadow said.

The Dark Guardian swung it's warhammer at Thomas who backed away quickly. He had to get by, he needed to get to Lady and Big. Shadow lunged at the monster again and dodged the mallet allowing him to spindash into Dark Guardian's face knocking him back.

"He seems weaker." Sonic said.

"Guess he's not at full strength, or Shadow got stronger." Tails said.

Dark Guardian went to punch Shadow but missed.

"CHAOS SPEAR!"

He fired energy spears at the monster but they had no effect. Dark Guardian then swung again and knocked away Sonic who tried to attack. Shade teleported on top of him was about to pierce her leech blades through it's eyes but the monster grabbed her and threw into the side of Thomas. Metal flew at him forming an electric ball around him planning to shock the monster but once again there was no effect. Dark Guardian headbutted Metal to the ground. Shadow tried to kick him in the face but this time was struck by the warhammer.

"UGH! THAT DAMN HAMMER!" Shadow growled.

Finally Dark Guardian turned on Thomas, Kingape and the Boo and readied it's hammer.

"Oh no!" Thomas said.

As the monster swung, it's suddenly halted by a strange energy. Everyone watches as golden energy circled the guardian before wrapping him up.

"RRRRRRRRRRRRAAAAAAAAAAAAWWWWWWWWWRRRRRRRRRRRRR!"

"What's happening?" Shade gasped.

"Lady." Thomas smiled.

Suddenly Dark Guardian is illuminated in a bright golden light and screams in pain before flashing out of existence. Everyone is silent for a few moments before Kingape breaks the silence.

"WHAT JUST HAPPENED?" Kingape yelled.

"It was Lady...it had to have been her...she knew." Thomas said.

Suddenly his eyes start to glow golden and everyone looks at him.

 _"Hello Thomas...it's been awhile. I really want to see you...but first I need help getting rid of this monster as I am not a full power yet. Please help me."_

Thomas' eyes went back to normal and he blinks.

"Thomas what happened?" Sonic asked.

"She has subdued Dark Guardian...but she needs us to finish it off for good." Thomas said.

"Then let's go!" Sonic said.

Everyone turns to Shadow who's looking away with his arms crossed.

"What do ya say Shadow? All aboard?" Sonic came over to him.

Shadow glared at him, then the others. Shade and Metal looked like they wanted no part of him, Kingape and the Boo just stare. Thomas and Tails look uncomfortable but serious as well. Finally Shadow smirks and shut his eyes.

"Hmph...very well." Shadow agrees.

 _ **End of ARC 4.**_

 _ **To be continued in ARC 5: Crystalized Darkness**_


	9. Mephiles PT 1

ARC 5: Crystalized Darkness

Chapter 9: Mephiles PT 1

Kingape got in contact with one of the commanders asking for some support in guarding the buffers. Pale Payleaf sent 20 of his Metarex soilders to guard the buffers and the Boo called for more of the ghosts to guard as well. Ultimately the Boo decided to stay behind to help.

"I just hope the Metarex can keep Mephiles busy should he try to follow us." Tails said.

"We shouldn't be long." Sonic assured.

The mobains decided to hop on top of Thomas.

"Hold on Big and Lady, we're coming to save ya!" Sonic said.

Thomas unhooked from the freight car and whistled. Seeing he was too close to the buffers to easily activate them, he had to back up.

"Are you guys ready?" Thomas asked.

"Let's do this!" Shade said.

"Let's make it quick." Shadow said.

Thomas then charged for the buffers and everyone braced themselves as the rainbow-colored portal opened up and they teleport through into the Magic Railroad. The other Metarex and Boos were rather surprised.

 **The Magic Railroad...**

Everyone gasped at the beautiful scenery, gold dust flew all around them and raced across the golden rails. Thomas was glad to see this place again...this was definitely a good spot to relax and enjoy yourself, if it wasn't for the Dark Guardian being held somewhere around here.

"Wow...this place is gorgeous, reminds me of Planet Wisp." Tails said.

"I know...I could get used to this. Heh...what do you think Shadow?" Sonic asked.

"Hmph...it's okay. Nothing that special." Shadow crossed his arms.

Shade rolled her eyes and went back to admiring the view. Kingape had never been to a pretty place like this, he was used to only being in space. They came across the freight car that Big had road in, it was off the rails on it's side.

"Huh, so Big really did get this far." Sonic said.

"Lucky." Shadow said.

Finally they were arriving at the other end of the line, Thomas could hear Lady again.

 _"WATCH OUT THOMAS! HERE HE COMES!"_

Thomas was about to brake when he suddenly is forced to speed up and races through the buffers, Thomas had hoped he end up on a different line than the one with the cliff drop since there were multiple routes. Unfortunately as they entered out into Muffle Mountain, Thomas immediately is halted by Dark Guardian who suddenly returns just by the cliff. The mobians get ready to fight as Dark Guardian prepares to swing it's warhammer.

"PROTECT THOMAS!" Sonic shouted.

Shadow and Sonic jump first and spindash into Dark Guardian who jumps out of the way but staggers a bit. Apparently Lady's magic gold dust had weakened it a bit...that was a good thing. Kingape stayed in the cab while Tails tried to figure out Dark Guardian's weaknesses. Shade and Metal worked together to fight against Dark Guardian who started to swing his hammer wildly and hits Sonic who crashes to the ground.

"CHAOS SPEAR!"

Shadow makes a second attempt to use his spears, aiming precisely at the monster's eyes but the Guardian covers his eyes in time. Shadow figured if he used chaos blast it was destroy part of the mountain. Metal flies around Dark Guardian dodging a punch and a hammer swing and kicks the monster hard in the gut before charging into him with an electric orb. Shade teleported around the monster trying to confuse it.

"Hmm, Shadow you may have no choice but to use Chaos Blast. It's the only way!" Tails said.

"Is that dangerous?" Kingape asked.

"But this is Muffle Mountain, Lady is hidden inside...you need to be careful." Thomas said.

Shadow looked at everyone before Dark Guardian takes another swing with its hammer and knocks into the back of Thomas.

WHACK!

Thomas is jolted forwards nearly knocking Tails and Kingape out of the cab.

"THOMAS!" Sonic gasped.

"CINDERS AND ASHES!" Thomas gasped.

Like long ago, Thomas slips down the mountain and lands on a large steep hill. Shadow had to use his power now.

"I have no choice now! CHAOS BLAST!"

Shadow unleashes a blast of red energy so powerful it indeed destroyed a bit of the mountain but also knocked Dark Guardian off the mountain and he tumbled down the hill.

"AFTER THEM!" Shade shouted.

Tails and Kingape humorously tumbled around the cab constantly smacking into each other and apologizing each time. Thomas knew he was heading towards the hidden buffers and could sense Dark Guardian now chasing after him. Tails grabbed the chaos emerald not scorched by the fire in Thomas' firebox.

"Thomas! Use the emerald's power!"

"Okay! Chaos-"

But before he could finish, Dark Guardian grabs onto his bunker just as Thomas dips into the ground and another rainbow-colored portal opened and sucked him and the Dark Guardian in. Sonic, Shadow, Shade and Metal end up getting left behind.

"Oh no!" Shade said.

"Damn it!" Sonic stomped a foot.

"What now?" Metal asked.

Shadow felt the ground, its energy connecting with his own. He pulled out his green chaos emerald.

"CHAOS CONTROL!"

The four are then teleported away.

 **Burnett Stone's Workshop...**

Thomas, Tails, Kingape and Dark Guardian end up racing through a large tunnel and Dark Guardian trips and falls hard onto the ground...he was too weak, yet he crawled forwards. Thomas sped closer to the light and spotted who he had been wanting to see for a long time.

"Lady."

"Hello Thomas."

There was Lady, the magical engine that kept life on Sodor, and next to her was Big and Froggy.

"Hi Thomas!" Big waved.

"BIG!" Thomas smiled.

Tails and Kingape jump out of the cab in awe at the engine.

"Whoa...she's...beautiful." Kingape said.

"So you're the magical engine?" Tails gasped.

"Yes I am...and it seems you were able to stop that monster." Lady said.

They all watch as Dark Guardian crawls weakily towards them, warhammer left behind on the surface of Muffle Mountain. Lady released some magic gold dust from her wheels and it surrounded Dark Guardian, its eyes glowing gold. But instead of destroying it, she manipulated its mind. Once finished, Dark Guardian just stood up and smiled.

"What did you do?" Tails asked.

"Consider it now your assistant in stopping that evil hedgehog." Lady smirked.

Thomas puffed closer.

"Lady...it's been so long...how are you?" Thomas asked.

"I'm fine, Burnett and Lily are still taking care of me. I heard about what you did last year. I'm very impressed...and proud." Lady smiled.

Thomas just blushed, just then the others arrive in a flash of green.

"Hah, we made it." Sonic cheered.

"Hey guys!" Big came over.

"Big you're okay." Shade hugged him.

Then they noticed Dark Guardian just standing there.

"Now to finish it for good." Metal said.

"NO!" Tails jumped on front of him.

"What do you mean?" Shadow asked.

"Lady manipulated his mind so now he can help us against Mephiles." Tails explained.

The four turn to Lady and gasp, though Shadow just crossed his arms. Sonic cleared his throat and smiled.

"Hello ma'am, I'm-"

"Sonic the hedgehog, I know all about you and your friends." Lady smiled.

Sonic blushed.

"So will you be able to help us be rid of Mephiles?" Shade asked.

"Indeed, though I'm not at my full strength yet since Burnett plans to head to Sodor and retrieve more Sodor coal for me. I should be back to normal by tomorrow." Lady explained.

"I just hope we have until tomorrow." Thomas sighed.

"Hmm, what if one of us was to go back now and get the coal, then you can be ready." Kingape suggested.

"That's a good idea...don't you think Kingape?" Sonic smirked.

Everyone turned to the metarex and he sweatdropped.

"Oh...wait...NO! WHY ME?" Kingape asked.

"Because you want to prove yourself...and this is your chance." Shade said.

While Shadow wanted to disagree, he knew he was in enough crap already, so he said nothing, the others just nod. Kingape heavily vented and clenched his fists tightly.

"Very well...I'll do my best." Kingape said.

And so as Lady's eyes glowed gold, Kingape is transported back to the Island of Sodor by his ship. He looked around to see no one, he had to be careful in case Mephiles was around, maybe one of the other Metarex commanders could help. Back inside the workshop, everyone was getting to know Lady while Shadow had an idea.

"Hmm...I think we should also try to find the Chaos Emeralds. Maybe they could enhance the power of the gold dust." Shadow thought.

"Huh, nice thinking Shadow. But that could take forever." Sonic said.

"Not necessarily, I think I can help locate where they could be." Lady said.

"Really? You can do that?" Tails gasped.

"Yes...just give me a minute."

Lady shut her eyes as her whole body glowed gold. After a few moments she returned to normal.

"Apparently Mephiles got a hold of them, and scattered them around the island. I sense him lurking around the Island for us, and sending out more villains from your past...and one from Shadow's." Lady said.

Shadow realized who she was talking about.

"You got to be kidding me." Shadow face-palmed.

"I wonder how far away each one is." Metal said.

"Looks like we need to get back to the Island fast, we need those emeralds back. We have only 2." Sonic said.

Lady then had rings made out of gold dust be places on a finger of each other them...except Dark Guardian of course.

"What are these?" Tails asked.

"These rings will allow you to use the gold dust's power against any foes you meet, but they won't be enough to stop Mephiles." Lady said.

Suddenly Dark Guardian turns into gold dust and is absorbed by Sonic's ring.

"Nice upgrade, I can even call the big guy if I wanted to." Sonic smirked.

Thomas let off some steam.

"I'll be back for you Lady, I promise." Thomas said.

"I'll be fine Thomas, I don't think Mephiles has a chance against me anyway. I'll keep in touch with you telepathically." Lady said.

With that, Lady sent them all back to the Island. Sonic got their attention.

"Okay everyone, spread out and search for those emeralds, we'll meet back at the buffers when we have them. Thomas, try to round up any engines to help search." Sonic said.

"You got it!"

Thomas and Shade set off to first find Tikal, Chaos and Percy who was probably out with the mail, Sonic and Metal went together to search while Shadow went alone, Tails and Big decided to go make sure Kingape was doing okay. The fact that Mephiles could be lurking around filled him with fear, Shade remained silent as he looked out the windows of the cab. Owls hooted and the wind blew against the trees making them rustle.

"Thomas you okay?" Shade whispered.

"I'm fine...I have to be brave." Thomas said.

Shade knew this was difficult for Thomas to handle...but she knew something that always cheered him up.

"You're a really useful engine Thomas."

That did make Thomas smile and feel a bit better...at least for awhile. So far he had come across none of the engines, where were they?

 _"Ooohhhh Thomasssss..."_

Thomas didn't dare say a word since he knew who the voice belonged to. Shade kept her mouth shut and ducked from the windows.

 _"I'm coming for you."_

Still the two said nothing and kept racing through the night.

 _"You're mine..."_

Thomas hoped he would come across someone soon, and before he had thoughts of screaming, he could see Percy up ahead at Elsbridge Station taking on water. He didn't have the mail with him instead he had a coal truck filled to the top. Thomas could hear a faint laugh from Mephiles before he stopped next to Percy.

"Hey Percy, I thought you were taking the mail." Thomas said.

"Oh Paxton volunteered to do it instead." Percy said.

"So what's with the..."

Thomas immediately realized what he was doing as Percy winked. Hiding in Percy's cab was Kingape, Big and Tails who had collected the coal. Thomas and Percy then made a false accusation.

"You taking that lost coal truck back where it was before?" Thomas winked.

"Oh yes, someone decided to try and hide it. Luckily I found it, well I should be off." Percy said.

He quickly and left and Thomas and Shade continued on.

"Yes...coal collected." Shade whispered.

A few minutes later, Thomas was still curious as to where Tikal and Chaos were, probably still scoping out sights to finish their movie. Unfortunately is searching was rudely interrupted when he could sense someone following him...Mephiles. The crystalized hedgehog was floating closer behind him. Shade was taken by surprise when Mephiles suddenly jumped into the cab to face her.

"Hello girl." Mephiles said.

Shade got in a fighting stance.

"Mephiles...what are you up to now?" Shade said.

"Oh just seeing if you really can collect the chaos emeralds...after all, I still have a surprise for you all while you collect them. Even if you get all 7, they won't do you any good against me." Mephiles chuckled.

"We're gonna stop you!" Shade growled.

"Keep thinking that, besides, none of this has to happen, simply hand over the secrets to the buffers...and you can become my SLAVE INSTEAD OF BEING DESTROYED!" Mephiles growled.

"NEVER!"

"VERY WELL!"

Mephiles jumped back out the cab and clenched his fists to his chest as he began to summon someone. Down the main line, a purple portal opened up and out comes a red muscular monster with large horns and a long red tail.

"Thomas, meet Zavok, the leader of the Deadly Six..." Mephiles said.

Thomas and Shade could see from Zavok's purple eyes that he was possessed and he was holding one of the chaos emeralds. They needed that emerald, but Shade didn't know if she could beat him.

"We'll still find a way to beat you Mephiles." Shade growled.

"Oh I'm sure you'll try...but he's not the only one." Mephiles chuckled.

Another purple portal opened up to Thomas' left and out came a floating demon-like alien with three glowing eyes, twin horns sticking out of both sides of his head and robe covered in chains. He was possessed as well.

"This is Black Doom, he's from Shadow's past." Mephiles said.

"Woah...this is not good." Shade said.

And finally to their right came a villain Thomas and Shade were all too familiar with, a certain robotic snake who tried to takeover the island last year.

"LYRIC!" Thomas growled.

"Not him again!" Shade said.

But like the other two, Lyric was possessed. As the enemies closed in on them...Mephiles floated down in front of Thomas.

"Now I bet you think I'm gonna send all three of them on you at once eh, well I'm not. I'll play fair by doing it one at a time." Mephiles said.

He made Lyric and Black Doom flicker away leaving only Zavok who finally spoke.

"Let's play a game shall we...it's called SCRAP THE LITTLE BLUE ENGINE!"

 _ **To be continued...**_


	10. Mephiles PT 2

Chapter 10: Mephiles PT 2

Thomas and Shade waited to see what Zavok had planned to do first. Mephiles laughed as Zavok backed away getting ready to charge. Thomas wanted to reason with him.

"Um Zavok right? Look it doesn't have to go down like this...you need to fight the control." Thomas said.

But Zavok only roared in response.

"I don't think he cares Thomas." Shade said.

"Well I tried." Thomas said.

Zavok then charges Thomas with a fist reeled back. Thomas gasped and sped backwards. Mephiles followed wanting to see how this went down.

"RUN! RUN YOU LITTLE BLUE PEST! IT'LL ALL BE OVER SOON!" Mephiles laughed.

Thomas needed to get onto another line, Shade kept watch of what was behind them.

"Track is clear Thomas, we need to get away from Zavok, then again he has the chaos emerald." Shade said.

"Hmm, I wonder if these guys are any good at racing, I used to not be so fast...but after all the crazy chases I've been involved in...no doubt I could keep ahead while we get that emerald." Thomas smirked.

"We can try, but we need to be going forwards first." Shade said.

Zavok caught up and swung his fist but Thomas reversed onto another line just in time. Zavok had to slow down giving Thomas a chance to stop and run forwards on the other line.

"GET BACK HERE!" Zavok yelled.

"IT'S NO USE THOMAS!" Mephiles yelled.

Zavok was now chasing after Thomas again and they bolted down the main line, Thomas wasn't going to stop for nothing now. Shade looked down at the ring on her gloved finger.

"Hmm...you think I can summon one of the others for assistance with the ring?" Shade asked.

"It's possible. Maybe we can even teleport to other areas. I don't need the island more damaged as it is." Thomas said.

"OH I'VE DONE ONLY A DEMO OF MY PLAN!" Mephiles yelled.

Suddenly Thomas and Shade see total destruction of several areas around the island, more destroyed stations, houses, trees and much more. Some fires had started as well injuring many people. Thomas hoped the Sodor Search and Rescue Team would help out, if they're weren't derailed or hurt.

"NO!" Thomas gasped.

"OH YES!" Mephiles said.

"YOU MONSTER!" Shade growled.

Thomas sped up fast as Zavak punched the back of him, Shade had to keep her balance.

"Okay, time to get some help." Shade said.

She focused the ring's energy and summoned Sonic who at first was confused by his surroundings.

"Huh? What's going on?" Sonic asked.

"THAT!" Shade pointed behind her.

Sonic saw Zavok and smirked.

"Oh yeah the Deadly Six leader, hah this should be easy." Sonic said.

"Are you sure?" Thomas asked.

"Just watch."

Mephiles floated down next to them just as Zavok punched the back of Thomas again.

"WHERE DID YOU GET THOSE RINGS?" Mephiles growled.

"None of your business." Sonic said.

He tried to spindash into Mephiles only for the crystalized hedgehog to rise up higher.

"IT'S THE WORK OF WHATEVER IS BEHIND THOSE BUFFERS ISN'T IT!" Mephiles growled.

Nobody said anything and Sonic only clenched the fist with the ring on it causing it to glow.

"TIME TO TAKE THIS FIGHT OUT OF HERE!" Sonic said.

"I COULDN'T AGREE MORE!" Mephiles said.

He suddenly absorbs everyone in a purple orb before they all vanish...but where did they go?

Back with Percy, he, Tails, Kingape and Big were on their way back to the magic buffers with the coal. They were surprised at how easy it was for them to get done.

"That was shorter than I thought." Big said.

"At least it's done." Tails said.

"Hey...what's that?" Kingape asked.

Another large purple portal opened up down the line and out came King Arthur again, this time with his horse.

"OH NO NOT AGAIN!" Kingape panicked.

"We can beat this guy!" Big figured.

"I hope you're right!" Tails said.

Percy screeched to a stop right in front of the horse who breathed on his face.

"HAH! You thought I was gone forever huh? Well too bad, now I shall finish you off for good, it should be easy enough." King Arthur said.

Percy had to think of a plan, they were still a bit far away from the buffers, but King Arthur was blocking their way.

"I bet I'm way faster than that horse." Percy smirked.

"Hah, you don't look like you could do anything helpful for your friends, you're small...much too young as well." King Arthur snorted.

Percy didn't like that one bit and neither did the others.

"I'll show you I can do this." Percy said.

He then moved forward causing King Arthur to move into the sky and race ahead of Percy. The horse galloped faster and faster as King Arthur turned to the side.

"YOU REALLY THINK YOU CAN DEFEAT ME? JUST TRY IT!" King Arthur growled.

That's when Tails and Kingape realized Big had a serious look on his face.

"Let me do this." Big volunteered.

"Big are you sure, you can get hurt." Tails said.

"No...I want to help." Big said.

"You know what, I'll join you." Kingape said.

Tails just watch baffled as Big and Kingape climbed on top of Percy. Big brought out his lure and activated the ring on his gloved finger before his lure was absorbed in the magic gold dust turning it into a large sword covered in titanium armor. King Arthur laughed.

"I despise fake knights...but if you're so determined, then so be it." King Arthur took out his sword.

The plan was for Big to weaken King Arthur, then Kingape would attack him from the front. They all knew the fight needed to be finished before they got to the buffers. King Arthur began the fight by releasing red orbs from his clawed hands and fire them at Big. Big readied his lure-turned-sword and bashed the orbs back to the king.

"OW! WHAT? THAT'S IMPOSSIBLE!" King Arthur roared.

"Sorry, but you're evil." Big shrugged.

"AAAARRRRRRGGGGGGGGHHHHHH!"

He then placed his right arm through a portal and another opened in front of Big. His arm came out with his sword and he started to slash it wildly at the cat. Big guarded himself and the ex-king's sword clashed with Big's sword. Failing, the knight retracted his arm giving Kingape the chance to lunge and wrestle the ex-king for the sword. The horse struggled with the added weight but got worse when Big jumped into the scuffle as well. The horse loss it's balance and fell onto the tracks. King Arthur, Big and Kingape roll away still fighting over the sword.

"GO, WE GOT THIS!" Kingape yelled.

Percy and Tails raced ahead into the siding and Percy got to visit the Magic Railroad for the first time. With the fight, Kingape gets launched away and now must deal with the horse. The horse angrily charged him and Kingape managed hop onto it sunk his claws into the unarmored places drawing blood. Big and King Arthur were fist-fighting nearby, but Big was quickly losing since he was being punched by metal fists.

"STUPID CAT!" King Arthur growled.

Big staggered around after getting punched several times, but he wasn't giving up. Big was much stronger than many thought, sure he was dim-witted, but he was still determined and brave. His own punches actually hurt King Arthur who was surprised. Froggy watched from nearby worried.

"I'll...I'll still fight." Big growled.

"AND DIE!"

King Arthur punches him for like the 10th time knocking the cat down and coughing up blood. King Arthur then watches in horror as Kingape brutally slaughters the horse by slashing it wildly with his claws and it exploded in purple dust.

"NNNNNNOOOOOOOO! YOU FOOLS!" King Arthur roared.

Out of anger he gets ready to stomp on Big's head when suddenly, a dark blue blur races right through his chest causing him to explode also in purple dust. Kingape quickly wipes the blood of his claws and runs over to help Big up.

"You okay Big?" Kingape asked.

"Oh...I'm gonna have a headache soon." Big groaned.

Froggy hopped into his hands and he cradled him.

"What was that blur, it looked like Sonic." Kingape said.

"You could say that..."

Suddenly the two turn to see the killer standing nearby, his back turned to them. It indeed looked like Sonic...but...a bit darker.

"Sonic...you okay?" Big asked.

The two walked closer to 'Sonic' and Big put a hand on his shoulder. 'Sonic' then turns around...and smiles.

"You good?" Kingape asked.

Then the most creepiest thing they ever saw happened, Sonic's eyes turned black and his pupils went red. His mouth opened to reveal yellow razor-sharp teeth. Though he was still wearing his gloves, his fingers had turned into razor sharp claws.

"You...you can't be Sonic." Kingape gasped.

The hedgehog then spoke...but it was demonic.

"I look like him yes...but...I'm from another dimension, ripped from it by that crystalized bastard...you can call me Sonic...just add...EXE."

But before the others could say anything, the demonic hedgehog fainted on the spot, he was apparently weak. Big and Kingape turned to each other.

"What should we do?" Big asked.

 **Green Hill...**

Thomas, Shade and Sonic had been sent to Green Hill were they were racing against Zavok who was almost defeated as well. Shade used her ring to produce gold-dust tracks for Thomas to race on through the zone. Zavok had tried to punch the ground to topple Thomas over or ram into him from the side but Thomas was too fast for him. Sonic and Shade remained on top of Thomas as he zoomed up and down hills, sped through loops and flew over gaps.

"WOW! THIS IS FUN!" Thomas yelled.

"Yeah, it's a pretty classic place to run." Sonic shrugged.

Zavok was getting more irritated but tired and Sonic found his chances to home attack into his head.

"STOP THAT!" Zavok yelled.

"HAH! KEEP DREAMING!"

Sonic home-attacked him one last time knocking Zavok back into multiple trees. Enraged, Zavok flew into the air and managed to past Thomas this time and was prepared to stop Thomas himself. Thomas didn't hesitate to ram right into Zavok pushing him onwards. Zavok's claws dug into Thomas' sides.

"I'LL END YOU!" Zavok yelled.

"NOT TODAY!" Thomas yelled.

Sonic smirked and looked over at Shade.

"You thinking what I'm thinking?"

"Oh yeah."

Together, the two summoned back Dark Guardian and Thomas braked hard making Zavok think he was winning. When he stopped, Zavok laughed.

"HA! I KNEW I WOULD STOP YOU!" Zavok said.

"Um...think again." Thomas smirked.

Suddenly Zavok is sucker-punched by Dark Guardian who roars at him. He was much bigger than Zavok and had his warhammer back.

"Oh no." Zavok gasped.

The others shut their eyes as Dark Guardian pummeled Zavok before launching him far into the sky with his hammer and he twinkled out of sight, presumably back to Lost Hex. Shade caught the chaos emerald Zavok had dropped. Mephiles returned enraged.

"DAMN IT! I THOUGHT HE HAD YOU!"

"Thanks for your help Sonic." Shade said.

"No problem, back to the island I go, I know who'll come in handy next." Sonic winked.

He used the ring to absorb Dark Guardian and warped away being replaced with Shadow.

"What? What's going on?" Shadow asked.

Mephiles then warped them all to a new location.

 **The Ark...**

They all ended up back on the looped circuit under the ARK and Mephiles summoned a possessed and revived Black Doom, much to Shadow's horror.

"Oh no." Shadow face-palmed.

"I'm sure we can take him this time. Mephiles doesn't know how these guys normally use their powers, so they must be weaker." Shade said.

Thomas continued to travel on the gold-dust rails as they raced around the track, Thomas remembered racing Dark Oak around this last year, the same rule still applied, capturing those energy cores...or so he thought he had to.

"Shadow, keep him distracted, I got a plan!" Shade said.

Shadow leaped on top of the cab and started to fire his Chaos Spears at him. Black Doom didn't seem to care that it was Shadow he was fighting. Shade used the ring to create a golden barrier around Thomas that was strong enough to protect them anything, even Mephiles' powers. Black Doom started to fire Swift Strike but it only bounced off the shield.

"WHAT?" Black Doom gasped.

"Hmph...try again." Shadow challenged.

Black Doom then summoned meteors and threw about 20 at them, but they also just bounced off the shield. Thomas managed to collect 2 energy cores along the way and felt the massive amount of energy surround him. Shadow teleported next to Black doom, used his ring to enhance his chaos powers and unleashed-

"CHAOS BLAST!"

Black Doom is launched far ahead of Thomas and bounces onto the circuit.

"EERRGGHH! HOW DID...WHAT?"

He had no time to react when an overcharged Thomas comes crashing into him so hard the alien demon exploded into the purple dust.

"Hah...too easy." Shade cheered.

Thomas eventually got back under his own power and Shadow smirked as Shade caught the next 2 emeralds.

"Not bad Thomas...not bad at all." Shadow said.

"Thanks Shadow." Thomas said.

"Hmph...I guess I was wrong about you. Just don't let me have to assist you again...I think you all got this covered." Shadow said.

Shade nods and Shadow warps away after giving Shade his emerald.

"Guess he really has changed...a bit." Shade scoffed.

Mephiles came down even more enraged.

"I CAN'T BELIEVE THIS! WELL I'M STILL NOT DONE!" Mephiles growled.

He sent them to the next location...one that was located in a bad future.

 **Stardust Speedway...**

Upon arrival, they saw they were now venturing down a rather skinny highway surrounded by large buildings and a red sky. Out of a large portal besides them came the possessed Lyric who starts to laugh.

"Haha! It's time to DIE!" Lyric yelled.

"Him again." Thomas groaned.

"Let's hurry this up." Shade groaned.

She then summoned Metal who materialized on top of the cab.

"Huh...wait are we...I remember this place." Metal said.

"Good then you can help us defeat Lyric again." Shade said.

"With pleasure." Metal growled.

He clenched his claws into fists and the ring glowed turning him into Neo Metal Sonic, Shade now had to look up at him.

"Ah yeah, I miss this form, LET'S GO LYRIC!" Neo Metal roared.

"RRRRRRAAAAAWWWWWWWWRRRRRRRRR!" Lyric screamed.

He snapped his claws and shot them at Thomas trying to punch him off the highway. Neo flew over and knocked the claws away before charging at Lyric and kicking him back.

"ARGH! YOU'LL PAY FOR THAT!" Lyric yelled.

He smacked Neo Metal away and lunged at Thomas slamming the road in front of him. Thomas in launched into the air doing a full front-flip before landing back on the magic rails. Thomas knew Lady would protect him. Lyric angrily charged up his claws and shot a large energy beam and Thomas made the rails twist and turn around them.

"UGH! YOU'RE CLEVER...BUT I'M SMARTER!" Lyric yelled.

He started to scare Thomas a few times by spiraling around the road, several times scraping his claws against Thomas' sides. Shade managed to jump onto Lyric's back and stab him with her leech blades.

"AAUUUGGHHH! GET OFF!"

He shook her off and she fell into Thomas' cab. Neo Metal came right over and fist-fought with Lyric all over the sky. They clashed in blurs of green and blue but neither of them gave in. Thomas and Shade looked for a way off the highway but it didn't look like it was ending anytime soon.

"Don't want to be part of that." Shade said.

"Yeah me neither." Thomas said.

After a bit more tussling, the Lyric and Neo Metal crash onto the road in front of Thomas and start rolling forwards in a ball of metal still fighting and swearing at each other. Thomas and Shade thought it was funny.

"You know I could watch this for another hour, but we need to get back to the island." Shade said.

The last 2 emeralds flew away from Lyric and Shade caught them.

"YES! WE HAVE ALL 7 EMERALDS!" Shade cheered.

"Now let's get back to Sodor." Thomas said.

"NOT YET!"

Mephiles appeared, he didn't look as angry as he should be...instead he was evilly laughing.

"You think I didn't have one last surprise left in store you fools? It's time you finally die!" Mephiles said.

Without warning he sent Thomas, Shade, Neo Metal and Lyric to what Mephiles thought was the last location.

 **Zone Unknown...**

When they arrived, they found themselves on a large cliff...seemingly in the middle of nowhere. It was a cloudy night and little wind was blowing.

"Where are we?" Shade asked.

"I don't know...there's nothing else around but those mountains in the distance." Thomas said.

The magic gold-dust barrier wore off much to their dismay. Shade looked at Neo Metal and Lyric to see they were still fighting behind them, Lyric had been freed of his possession thanks to Mephiles giving up on him and now Lyric was just angry with Metal.

"Will you two knock it off already?" Shade groaned.

"NO!" They shouted.

But the fighting did cease when the ground below began to rumble. Down below was a large pool of lava and something was about to rise up out of it. When it did, it made Shade's heart skip a beat and Thomas lower lip quiver. The monster was massive and had about 7 eyes with one being the biggest one right in the middle. It had 6 arms with long sharp claws and was glowing purple meaning it was a clone.

"What...what is that..." Thomas gasped.

"I have no idea." Shade whimpered.

Mephiles appeared and laughed loudly.

"HA-HAHAHAHAHAHAHA! AAAHAHAHAHAHAHAHAHAAAA! YOU FOOLS...THIS IS DARK GAIA...YOUR DOOM! HE COULDN'T BE DEFEATED BY RUNTS LIKE YOU! AND ESPECIALLY YOU THOMAS THE TANK ENGINE...YOU SHALL PERISH FIRST!

Then the most horrifying thing to happen in Thomas' life happened, Mephiles fired a white beam from his hand...and it hit Thomas right in the face, the force knocking Shade away. Thomas flew back and smashed into the mountain behind him. From Dark Gaia's view, it was like throwing a toy into a wall. The blast disintegrated Thomas' whole face, crunched up his body and ultimately killed him and he slid to the ground. Lyric and Metal were speechless, Shade ran over crying.

"THOMAS? THOMAS! **THOMAAAAAAAAAASSSSSSSSSSSS!"** Shade roared.

 **Island of Sodor...**

Sonic, Shadow, Big, Kingape, some Boos and all 4 Metarex bosses were gathered outside Pale Bayleaf's battleship where Sonic-EXE was recovering from some strange corruption.

"I assume Mephiles was trying to find some of the most evil beings from different dimensions and found him, but like Dark Oak, he couldn't control him forever. I guess this hedgehog is still in some pain from Mephiles attempts for control.

"I really hope out master is okay...where could he be now?" Black Narcissus wondered.

"Maybe that magical engine can bring him to us." Red Pine said.

"UGH! TOO MUCH IS GOING ON!" Yellow Zelkova grabbed his head.

"I hope Tails and Kingape got that coal safely to Lady." Sonic said.

"Lady should be here soon I'm sure." Shadow said.

"But what about Thomas, Shade and Metal?" Big asked.

"Oh man...we need to find them." Kingape said.

Then suddenly Tikal and Chaos race over in a panic and Tikal grabs Sonic's shoulders.

"Sonic...we have a problem." Tikal said.

"What is it Tikal?" Sonic asked.

"It's Thomas...there was...an accident." Tikal sighed.

Sonic's eyes grew and everyone else gasped.

"What kind of accident?" Shadow asked.

Tikal gripped Sonic's shoulder tighter, everyone came closer including the 4 Metarex bosses.

"Tikal?" Sonic said, a tear coming down his face.

"Mephiles summoned some large 7-eyed creature..."

"Dark Gaia?"

"Yes...and...then...Mephiles...he...he..."

"TIKAL DON'T TELL ME..."

"I'm sorry Sonic...Thomas has been killed."

Everything went silent...and Sonic dropped to his knees...no one even noticed that the demonic hedgehog had woken up...the evil copy just frowned.

"Darkness has risen..."

 _ **To be continued...**_


	11. Mephiles PT 3

_**Finally we've reached the last chapter of this story. I am very satisfied with how many more ideas went into this one than the previous story. Anyways, time to end this and find out the fate of Sodor!**_

* * *

Chapter 11: Mephiles PT 3

It took about 5 minutes for Sonic to fully register what Tikal had told him. Her hands remained gripped to Sonic's shoulders as the hero was on his knees looking down letting his tears slip to the ground. A few sniffles escaped Sonic as Big rubbed his back. Choas just crossed his arms and shook in head in complete shock over this event. Shadow looked away closing his eyes. The Boos sighed and looked at each other. Kingape and the Metarex bosses didn't know what to think. Excluding Kingape, the bosses hated Thomas...but they weren't the ones that killed him. And now that he was gone, the Metarex felt...uneasy.

"Sonic...we have to rely on Lady now. Maybe she can revive him." Tikal assured him.

But Sonic thought differently...he could feel a darkness inside him growing...a hidden anger and malice consume him. Tikal could feel the energy in Sonic changing rapidly and she stood back.

"He...killed Thomas...he...he..."

"Sonic calm down...we need to think this through." Shadow said.

"How...can I...think about a plan...when..."

Sonic gritted his teeth and his fingers gripped the floor. A dark aura began to surround him...Shadow remembered how this had happened last year.

"Oh no." Shadow thought.

"Sonic you shouldn't be giving up now, that's not what you heroes usually do." Pale Bayleaf said.

"We'll admit you're not weak, there's always some kind of plan to be made." Black Narciussus said.

"Uh...guys why is that other Sonic copy awake already." Yellow Zelkova asked.

"What? What are you-" Red Pine cuts himself off.

Everyone except Sonic turns to his demonic copy who is now standing with his head tilted and mouth open revealing his yellow sharp fangs. He is also floating off the ground and smiling big.

"He's feeling the true anger inside him...he should embrace it." Sonic. EXE sneered.

"He's need to get under control before something he does something stupid." Shadow said.

Sonic. EXE just turns his head towards Shadow and keeps it tilted at a creepy angle.

"Why? It's too late to change him...even I can feel his rage...I am him after all. Unlike you FAKER!" Sonic. EXE laughed.

Shadow growled but knew this was no time to fight. Besides unlike him, Sonic. EXE managed to heal from Mephiles' powers in a short time and could not be controlled. Seeing Shadow wasn't going to make a comeback, Sonic. EXE floated over to Sonic who was slowly turning into Dark Sonic, his pupils and irises were already gone and only his white eyes remained. Sonic. EXE then put his clawed hand on Sonic's shoulder.

"Embrace your anger Sonic...after all...we all want revenge on Mephiles for everything he's done. All the murder, the destruction...especially your friend Thomas." Sonic. EXE sneered.

Dark Sonic finally got up and faced him, everyone else backing away.

"How can I trust you? You're evil, you're an evil spawn of me from another dimension. How do we know you'll just try to takeover when he's dead?" Dark Sonic asked.

Sonic. EXE scoffed and put his hands on his hips.

"You think I want to be here? I only care about getting revenge on that crystallized punk and getting back to killing and torturing in my own world. I'm willing to become good just this once." Sonic. EXE said.

Tikal bravely stepped up to Sonic. EXE, almost getting smacked by Sonic. EXE's longer spins.

"Please Sonic. EXE, why do you have to torment people? What purpose is there?" Tikal asked.

Sonic. EXE turns to her with a frown.

"It's my business, and it's the only thing that makes me happy. And still continue to do it, consider you all lucky." Sonic. EXE growled.

Tikal touch the demonic hedgehog's hands and felt the strong evil energy in him.

"I see." She sighed.

 **Muffle Mountain...**

Tails and Percy had arrived at Lady's workshop where the magical energy had felt a great disturbance in the force. She sensed Thomas no longer alive.

"It can't be...no...IT'S NOT TRUE!" Lady gasped as tears formed.

Percy was confused by her outburst. Tails was busy shoveling the Sodor coal into her firebox.

"What's wrong Lady?" Percy asked.

Lady looked up at him...she really didn't want to tell him, but she had too.

"Percy...Tails...Mephiles has killed Thomas." Lady cried.

Percy felt his whole body go freezing cold and Tails dropped the shovel he was holding.

"Thomas...is dead?" Percy whined.

Lady winced at Percy's cracking voice. Tails angrily punched the coal truck.

"Mephiles has really done it now." Tails said.

Percy could not believe what he had heard...his best friend was dead.

"NO! NNNNNNNNNNOOOOOOOOOOOOOOOO!"

Without warning Percy reversed out of the workshop much to Lady and Tails' surprise.

"PERCY WAIT!" Tails yelled.

But Percy didn't bother and raced through the tunnel and through the magic buffers. Tails quickly put one more pile of coal in the firebox and hopped into Lady's cab.

"LADY! WE NEED TO GO!" Tails yelled.

"Let's hurry!" Lady said.

She whistled and raced out of the workshop hoping Burnett Stone wouldn't notice she was gone. They had to catch up to Percy and save the others quickly.

 **Magic Railroad...**

Percy used the magic's power and turned himself around so he was racing forwards and needed to get back to the island. He needed to find Mephiles and make him pay, he didn't know how he would do it, but he would find a way. Lady however much faster than Percy and started to catch up.

"PERCY STOP! YOU'RE GONNA GET KILLED AS WELL!" Lady shouted.

"BETTER ME THAN THOMAS!" Percy shouted back.

Tails flew ahead and landed in Percy's cab, he needed to manually stop him before he reached the buffers.

"Sorry Percy, but it's for your own good." Tails whispered.

He put on the brakes making Percy slow down, but Lady accidentally rammed into the back of him and push him right through the buffers.

 **Island of Sodor...**

Once again the Boos and Metarex soilders were surprised to see Percy come through, but this time they were in awe over seeing the magical engine. Lady remained close behind Percy as they went down the line.

"Percy please...I can sense where Thomas, Shade and Metal are, I'll get them. But I need you and Tails to get the others." Lady said.

They finally stopped at a destroyed Knapford Station. Percy sighed.

"I'm sorry...it's just...why does this have to happen?" Percy asked.

"I don't know...but know this Percy, he won't be dead forever." Lady assured.

This made Percy smile a bit, Lady smiled as well.

"Now go find the other engines, Tails go find Sonic." Lady said.

"Yes ma'am the boys said and they left. Lady then teleports away.

 **Location Unknown...**

Shade, Metal and Lyric were still fighting against the monstrous Dark Gaia while Mephiles had gone back to the Island leaving them to their doom. They had dragged Thomas' body to a safe place out of the way. Shade had teleported towards the monster and stab 2 of it eyes. Neo Metal Sonic had pierced two others. And Lyric managed to bash away any incoming meteors and evade the claw swipes of Dark Gaia long enough to destroy 2 more. This left only the one major eye that was open in the middle. But they were losing thanks to getting hit by the claws and even more meteors.

"UGH! WE CAN'T REACH THAT EYE!" Shade growled.

"HE'S TOO POWERFUL!" Metal yelled.

"There's nothing else we can do!" Lyric thought.

"Why are you even helping us to begin with?" Shade asked.

"DO I LOOK LIKE I'M TRYING TO DIE?" Lyric argued.

Suddenly Lady appeared beside them in a flash of gold dust and was surrounded in a golden aura barrier. The three could not believe what they were seeing.

"Lady!" Shade gasped.

"You're here!" Metal gasped.

"Who are you?" Lyric asked.

"There's no time for introductions...we need to stop this beast now!" Lady said.

"How?" Shade asked.

Lady closed her eyes and made all three of them be consumed in a golden aura. They felt much more powerful.

"Hey...all this energy...is empowering me." Metal said.

"I feel GREAT!" Lyric said.

"Now we shall be able to bash through anything Dark Gaia has to throw at us. LET'S GO!" Shade said.

The three nod and flew together towards the massive eye. Dark Gaia angrily tried to swipe at them but his claws bounced off them and so did the meteors. As soon as they made contact with the eye, it explodes and so does the rest of him turning into a massive cloud of purple dust. Lady noticed Thomas' mangled body nearby, she could barely look at him in that condition.

"Come on Thomas, I'm gonna take you home." Lady said.

When the three came back...they saw Lady couple up with Thomas' body.

"You can fix him right?" Shade asked.

Lady only nods and Metal rubs Shade's shoulder. Then all the attention is put on Lyric.

"What? I can't join in for once?" Lyric pouted.

Suddenly they hear someone screaming from the sky, looking up, they spotted Dark Oak falling down and he lands right on Lyric tackling him down. When they got up they nearly got to fighting when Shade stopped them.

"Dark Oak where did you come from?" Shade asked.

"I was trapped within that monstrosity." Dark Oak dusted himself off.

"Huh? Mephiles sure is weird, BUT WE'RE GONNA KILL HIM!" Metal growled.

"Come, let's head back to the island." Lady said.

 **Island of Sodor...**

Everyone had gathered outside the battleship where Tails was explaining a few things...and of course he was freaked out by Sonic. EXE.

"Uh...so you killed me in your dimension?" Tails asked horrified.

"Ah yes...you were one of my first victims. Don't make yourself the first in this one!" Sonic. EXE sneered.

Sonic was still in his dark form but was able to control himself...at least a bit.

"YOU KILL HIM AND I'LL WRING YOUR NECK!" Dark Sonic warned.

"Relax I'm just joking." Sonic. EXE rolled his eyes.

"Hey look!" Big pointed out.

Everyone watched as Lady, Shade, Metal and Lyric arrived with Thomas and Dark Oak, but they didn't say anything.

"Lyric?" Dark Sonic gasped.

"Long story." Lyric said.

Dark Oak caught the Metarexs' eyes and they gasped.

"DARK OAK SIR!" Kingape gasped.

Bayleaf and Narcissus quickly raced over and helped the limping leader towards the others.

"Sir are you okay?" Pine asked.

"I'm fine...I'll recover. Just glad to be rid of that hedgehog for now." Oak snarled.

"Finally we're back together again." Zelkova cheered.

Everyone else just stayed silent as Lady pulled Thomas' body towards them, the sight of him caused Sonic's dark side to slowly vanish and he returned to his normal blue self...but now sadness took over. Tails covered his mouth in shock, Big and Kingape just gasped, the Metarex bosses just grunted in disbelieve. Tikal clasped her hands together and Chaos rubbed her shoulder. Percy then arrived to see Thomas.

"All the engines are safe in hiding...but...Thomas..." Percy gasped.

"Percy, everything will be okay." Shade said.

Then she pulled out the seven chaos emeralds, they circle around Thomas and Lady unleashes some magic gold dust to cover the chaos emeralds increasing their power. Everyone watches as they began to circle faster and faster around Thomas and engulf him in a bright golden light. A minute later the light vanishes and everyone is dumbfounded by what they were seeing. There in the middle, living once more, was Thomas the tank engine, only now as Super Thomas. Percy moved closer.

"Thomas? Is that you?" Percy asked.

The gold and blue engine smiled.

"Hello Percy." Thomas said.

"THOMAS!" Percy whistled.

Everyone cheered, but it was quickly interrupted by a familiar evil laugh. Everyone turns forwards to see Mephiles standing there cracking his knuckles.

"So...you think you've beaten me huh? Sure you've gotten back the Metarex leader, you saved Thomas' body, and you defeated every single enemy I've thrown at you. But I STILL LIVE!" Mephiles yelled.

Sonic. EXE stepped up closer.

"YOU'RE GONNA PAY FOR SENDING ME HERE!" Sonic. EXE snarled.

"Hah, your pathetic! Just like the real sonic!" Mephiles pointed to the blue blur.

Then Mephiles noticed that Thomas was alive and golden.

"WHAT? HOW DID YOU COME BACK? I KILLED YOU!" Mephiles growled.

Thomas smirked as Lady moved closer.

"You can thank me for that!" Lady smiled.

Mephiles could quickly that mass amounts of golden energy in her, it almost made him stagger back.

"YOU! You must be who was stored in those buffers. Well then I guess I'll have to get rid of you in order to destroy this island completely. YOU'LL ALL BE DEAD VERY SOON! NO EXTRA POWERS WILL SAVE YOU NOW!" Mephiles growled.

Everyone got ready, of course except Percy who back a bit. Lady however was still smiling.

"Just go ahead and try." Lady said.

"Very well!"

Everyone was shocked at what happened next. Mephiles flew at Lady with a purple orb ready to smash into her face, however as he made contact, he is suddenly forced back and slams into the ground hard. Lady didn't even flinch as Mephiles rubbed his head.

"What? How is that possible?" Mephiles gasped.

"I'm much more powerful than you." Lady said.

"OH YEAH?"

Mephiles tried again planning to punch her, but the gold dust barrier bashed him back and he hits the ground again.

"Argh...NO! I CAN'T LOSE! THAT'S IMPOSSIBLE!"

Mephiles got up staggering around, he was feeling weaker. Sonic and Shadow immediately dashed at him and home-attacked him back down. Then Metal and Shade ran at him and sucker-punched him a few feet away.

"HOW? HOW AM I THIS WEAK! IT MUST BE THAT GOLD DUSTY STUFF SHE HAS ON HER! Such as amazing power...I'M GONNA CLAIM IT MYSELF!" Mephiles vowed.

He got up and tried one last time, but was met with defeat when Thomas rammed into him knocking him far down the line. When Mephiles tried to get up, he saw Sonic. EXE coming straight for him. For the first time, Mephiles actually felt afraid. Before Sonic. EXE could come in contact with him, Mephiles warped away.

"Ugh, where did he go now?" Sonic wondered.

"I think I know." Lady said sensing his signal.

"Where?" Sonic. EXE asked.

 **Radical Highway...**

Mephiles had chosen a place to hide thinking they would never find him. He ached and he felt so much pain. He had never been able to feel such pain before. He sat on top of bridge supports looking down at the city.

"I can't believe I'm losing. That engine is very powerful...ugh...why did I bother trying to bring people from other dimensions, in fact why did I bother getting help at all." Mephiles whined.

 _"MMMMEEEEPPHHHHIIILLEEEESSSSSSSSSSSSSS!"_

"Oh no!"

Mephiles looked ahead of the bridge to see Sonic. EXE standing there holding a thumbs up. Mephiles felt scared...his dark soulless heart feeling smaller and colder. Sonic. EXE had no heart...and no a soul...he collected them.

"WHAT DO YOU WANT?" Mephiles shouted from where he stood.

"So many souls to play with, so little time, wouldn't you agree?" Sonic. EXE laughed.

Mephiles shuttered and decided to run for it. He went to fly but realized he had his powers stolen by Lady and he plummeted to the ground crashing onto the concrete. When he got up, he saw Sonic. EXE standing right in front of him, his head tilted to the side and mouth open wide.

"Going somewhere?"

"GAH!"

Mephiles raced passed and ran for it on foot, but Sonic. EXE floated up next to him.

"Here I come." He teased.

Mephiles ran faster and the demon kept up. They raced up and down slopes, jumped a few gaps in the road, and zoomed through a few loops. Mephiles couldn't understood why the highway was built this way. Sonic. EXE would constantly disappear and reappear around him and taunt him.

"You're too slow!"

"SHUT UP!"

"You won't be ready for round 2."

"GO AWAY!"

 **"YOU'RE GONNA DIE!"**

"NO!"

Eventually they reach a long stretch of road and Sonic. EXE eagerly tackles him down. The two wrestle around for a bit before Mephiles gets on top and angrily starts to pummel him, but his punches took no effect and Sonic. EXE was laughing in his demonic way. Sonic. EXE claws Mephiles in the face before flipping them over, picking him up and pushing him away.

"I'M GETTING TIRED OF THIS!" Mephiles shouted.

"Oh I bet you are...WELL SO AM I!" Sonic. EXE shouted back.

The two angrily charge each other and collide and a massive explosion rocking the highway. A massive dust cloud engulfed the area for a few minutes. When it cleared, Sonic. EXE was still standing and Mephiles was lying on the ground coughing up blood.

"Ugh...no..." Mephiles clawed the ground.

"Aw...still not giving up are we?"

"FUCK YOU!"

Mephiles slowly got up and went to punch the demon who blocked it, then the demon punched him back twice. Dazed, Mephiles staggered back before EXE went behind him and held Mephiles in place.

"HEY WHAT ARE YOU DOING?"

"HOLD STILL!"

Suddenly the two see two blurs of gold heading straight for them. Mephiles recognized them and screamed in horror.

"NO! NO! NNNNNNNNNOOOOOOOOOOOOOOOOOOOOOOOOOOOO!"

Bolting for them was Super Sonic and Super Thomas smirking.

"Together?" Super Thomas asked.

"Together!" Super Sonic said.

It only took a second...during that second, EXE had warped out of the way, and Super Thomas and Super Sonic collide with Mephiles so hard, he ultimately explodes in a cloud of purple particles and fade out of existence, he was finally destroyed. Seeing he was gone, Sonic and Thomas cheered.

"HOORAY!" Thomas cheered.

"THAT WAS INCREDIBLE!" Sonic cheered.

EXE then comes over clapping.

"Nice work...took you two long enough." EXE said.

"Whatever, let's get back to the island." Sonic said.

 **Island of Sodor...**

After hearing the news, everyone decided to celebrate well almost everyone. Lyric has disappeared during the whole chaos presumably back to his base. The Metarex were also about to leave but Kingape wanted to say his goodbyes.

"It was nice working with you all, but it's time we revert back to our old ways." Kingape said.

"Heh, whenever your commanders want to fight, we'll be ready!" Sonic said.

Kingape actually hugged Big who hugged back, much to everyone's shock.

"Take care Big, you really proved yourself." Kingape said.

"Aw thanks. I did my best." Big said.

Eventually all the Metarex left with Dark Oak vowing to destroy Sonic and his friends another day. Then the Boos all retreated back to the mountains until the island was restored. This left Thomas, Lady, Percy, Sonic, Tails, Shade, Metal, Shadow, EXE, Tikal and Chaos.

"Hey so what happened to Dark Guardian?" Tails asked.

"Oh he was destroyed when the clone of Dark Gaia was destroyed." Lady explained.

"Hmm...well I guess everything is back to normal." Sonic smiled.

"Define normal." Shadow said.

Everyone saw there was a lot of destruction. But Lady let off some steam.

"Don't worry, I can put everything together again."

She closed her eyes and she began to glow, and instantly, the whole island was finally restored like brand new. No more fires, destruction, injuries or anything else like that. A few minutes later everyone recognized Sir Topham Hatt's car pulling up.

"Ah I see Lady here has restored everything! Well done! My, after so much chaos, I think there's gonna be a bright future ahead of us." STH said.

"Indeed sir, glad we could help." Shade said.

"Well done to you all, and Thomas, Percy, Lady, you three are really useful engines." STH said.

The three whistle happily, though it annoyed Shadow. STH didn't bother to question where EXE had came from.

"So EXE, you heading back to your dimension now?" Sonic asked.

"Yeah...although I may be back to see this movie Tikal and Chaos are making. How much longer?"

"It should be just 3 days. We should hold a movie night here on Sodor." Tikal suggested.

"That sounds like a great idea." Thomas said.

"Then we'll do it!" STH agreed.

"Hmph...I won't have time for that." Shadow looked away.

"Typical Shadow." Sonic rolled his eyes.

Shadow smirked before looking to Thomas.

"Thomas, nice work. You're learning...just remember who the ultimate lifeform is." Shadow said.

He walked away while everyone rolled their eyes.

"Hey Shadow, what about our race?" Sonic asked.

"Another time...you'll need rest since you're in no shape to beat me." Shadow smirked.

Before Sonic could retort the black hedgehog had warped away.

"Faker." Sonic muttered.

Meanwhile, Tails was confronted by EXE.

"So...you really are going to be killing more in your dimension?" Tails asked nervously.

"You bet...wanna join me?" EXE grinned.

Tails backed away.

"No thanks."

"Thought so...hehehe..."

He loudly laughed demonically before flickering away. Tails rubbed his head in relief, only to feel someone behind him. Turning around, EXE roars in his face before finally warping away. Tails just fainted on the spot.

Three days later, all the engines gathered at Tidmouth sheds where in front of them was a projector lighting up a large screen for the movie. Sonic, Tails, Metal, Big, Shade, Tikal and Chaos had invited EXE, Blaze and Marine to watch the movie which they were happy to do. Knuckles couldn't come since he was guarding the Master Emerald. Shade nudged Tails and gestured to Sonic and Blaze who were sitting next to each other, their gloved fingers slightly touching. Down below, Lady had warped herself besides Thomas.

"Thanks Lady for everything." Thomas said.

"You're welcome, you were very brave." Lady said.

"Just promise me one thing...you'll always be here for us...for me."

"I promise Thomas...I'll always be here for you all..especially for you."

 ** _THE END_**

* * *

 _ **And finally that ends the story! It's been quite awhile since I wrote the first chapter and this has definitely come a long way. Well, hope you all enjoyed this! There is now one last sequel called "Sonic Chronicles: Blue Steam" now available to read if you want. Anyways, KINGSTRIKER OUT!**_


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